Hi Rob, I'm not sure that I follow what you're trying to accomplish. Do you need your figures to appear in text, or do you need them to appear at the end of your document after the references section? (The way that many biomedical journals specify an article must be submitted.)
And what do you mean, by "the default order isn't what I want." Typically figures are printed in the order that they appear in the document. If you are doing fancy things with wrap-floats, that can throw the ordering of the figures off; but otherwise, whatever order you specify in your document should be the order they appear. Which means, that if you need them at the end of your document, then that is where I would place them (after the bibliography). You can then refer to them in the text by using a tag + cross-reference. If you need them to appear in your text at a particular position, then that is where you should place the float. There are ways to make floats go to the end of a document and arrange themselves into separate figures and tables sections, but it involves resetting LaTeX values and some ugly hackery. Cheers, Rob