What is best for your book will be up to you, at least at this stage.  An editor may have some suggestions later, but the architecture you create now--if you can articulate it, and point at it--will serve you well.  The following are some useful ways of thinking about organization, with the intent of letting your book show itself to you.  Try all of these, and listen carefully each time to what the newly gathered manuscript has to say.

a. Temporal Narrative suggests time as your editor.  This is an old, but often effective, approach.  Time orders things in an often unexpected but logical way.  Temporal narrative might be the order in which the pieces were written, the age of the speaker--if the manuscript covers a lifetime, or temporal indicators within the poems themselves.

Backward Temporal Narrative can also be effective.  If you walk along a hiking trail one way, and see certain things, returning along that trail ought to be equally coherent and connected, with the same view of things, but new.
"When you start with a portrait and search for a pure form, a clear volume, through successive eliminations, you arrive inevitably at the egg. Likewise, starting with the egg and following the same process in reverse, one finishes with the portrait."--Pablo Picasso

c. Character Growth employs a narrative that follows characters as they grow up or change, which can be effective if your manuscript has strong characters and is based on character development.  This long storytelling tradition would include the bildungsroman, or coming-of-age narratives.

Convergent Narrative offers two parallel stories of people who will be connected in some significant way, but who are not connected at the beginning.  The form may include more than two parallel stories, but there may be a point of diminishing returns if the complexity overwhelms the artistry.

The Trip is an old and honored form of storytelling involving a journey or quest.  Walk walk walk, drive drive drive, fight fight fight, talk talk talk.

Nature can be an organizing schema.  You might group your poems or stories by season or elements, literally or metaphorically.  Poems about fall, for example, would include anything that drops or expends energy.  Winter stories would include anything about dormancy.

Organic approaches are based on the physical qualities of the item described.  For example, a story about a zoo might follow the paths through the zoo and what you would see on each one of them.  A book of love poems might be organized by head, neck, clavicle, chest, and, uh, toes.

Link by Colors, by Smells.  We're talking about the senses here, but be loose or open in your sensibility.  Include a poem with a red object in it, even--and especially--if the word "red" does not come up in the poem, and pair it with another poem containing something else that is red in it.  Link stories or chapters by smells, by tastes, by senses we haven't even discovered yet.

Partnered or Thematic Grouping clusters all the poems about ice cream together.  Or all the stories with a single image or shared leitmotif may be clustered together.  Position them effectively: The first four poems contain the word "razor" and the fifth poem contains "sharp."

Orchestrated Structures link dissimilar ideas that share a single characteristic--not unlike the razor-razor-razor-razor-sharp sequence, though perhaps not as easy to decipher.  Rather than linking all the poems about ice cream, for example, it might simply be the joining of a group of pieces about Antarctica, the last look of a partner you've just broken up with, the broken icemaker in your Amana, and songs about Christmas.  The connection is clear--cold--but the circumstances are not at all necessarily joined.

Language or Issues or Big Thoughts are somewhat shopworn but viable ways to organize a manuscript.  But make sure you, rather than the issue, are writing the poems or stories.  Rhetoric is rarely good art or plot.  What should happen is far different from what does happen.  People live far more imperfect, and interesting, lives.

"The Twist was a guided missile, launched from the ghetto into the very heart of suburbia. The Twist succeeded, as politics, religion, and law could never do, in writing in the heart and soul what the Supreme Court could only write on the books."--Eldridge Cleaver

l. Logical Sequence involves identifying what a reader needs to know in order to understand the next thing, then ordering the poems or stories so that they make sense.  This is like climbing a ladder.  A detective novel works this way.

Spiral Structures are chains of associations based on similarity.  The spiral should be like a hawk circling slowly in and down.  The spiral structure is similar to the dialogue concept, with one line speaking to another in a long chain, but rather than circularity or closed dialogue, the movement is slowly and evenly forward.
"We shall not cease from exploration
And the end of all our exploring
Will be to arrive where we started
And know the place for the first time."
--T.S. Eliot

Mosaic structuring uses many small fragments to tell a larger story.  Like a mosaic, the individual pieces are bits of color and shape.  From a distance, as the reader stands back and puts them all together, a picture emerges.  A mystery is well-served by this form, though the process serves many kinds of manuscripts.  The test of this form is, of course, that something clear must emerge.

Objective Ordering may be appropriate depending on the subject of the manuscript.  If the book is about the anonymity of force, you might want to use untitled poems identified by only number.  You might alphabetize the poems by the first word.  You might throw the stories up into the air and order them according to the whim of their landing.  Objectivity, if you can truly live with it, suggests a sense of metaphysics--that something out there, rather than us, is in control--or the more troubling suggestion of what has been called pataphysics--that neither we nor anything else out there is in control.  Getting a reader to understand this, however, might take an author's note.

Alphabetizing is a strong but deceptive organizer, both whimsical and efficient at the same time--while being neither finally.  It simply offers an effective foundation for letting the manuscript speak for itself.  Related to Objective Ordering, it is an institutionalized version of throwing your poems up in the air and letting the order settle itself.  The trouble, of course, with these methods is that you will not be able to stick with them.  Something will trouble you, or you will want to just exchange one poem for another in the order, or like that.  Examine this feeling.  The ordering sensibility you are looking for may be resident in your inability to truly let objectivity order the manuscript.

Eccentric Structures involve oddities or non sequitur thinking linked together by virtue of their lack of connection.  Surrealism made a mighty attempt at this, and succeeded in large measure by finding value in what would seem at first meaningless and nonsensical.  Psychotherapy often plays in this garden as well.

r. Last-line-First-line Dialogue is the most whimsical and often the most fun.  See what the last line of a poem or story would connect to in the first line of another poem or story.  This will establish a dialogue among the pieces in the book.  Even though you may also realistically need to consider the second line and the second-to-last line, the idea is to forget about the body of the poem or story and just look at what the first and last lines have to say to one another.  This creates a coherent book in its in-between spaces, and gives a surprising sense of motion or connection in the moment--that is, connection where we do not expect to find it.

s. The Old Neighborhood is still something to count on, an indestructible, definable, visceral, and tangible home-ness.  I'm am talking here about place, which--if you know something about one--you ought to consider.  Geography is a natural connector, and exasperating separator.