With iAnnotate you can rearrange the page order of a document. To do so, open the Navigation Panel on the left and tap the Actions accordion, then select "Rearrange Pages."
A popup menu will appear with a thumbnail image for each page. If your document is long, you can scroll up and down to view more pages.
To move a page, long tap on it until it starts to wobble, then drag it to a new position. You will notice the other pages shifting out of its way as you drag. Release the page when you've got it where you want it.
You can move as many pages as you want in a single session. To confirm your changes, press the Done button. This process can take a few moments to finalize, especially for large documents with many changes.