To merge documents, please go to the iAnnotate homepage by tapping the + in the top left corner, then navigate to where the files are you'd like to merge, select the files, then tap "..." at the bottom and select Merge, you will get a chance to select the order to merge the files and then a new document will pop up with the merged files.  

If you'd like to move pages around, simply tap the four boxes at the top right with the file open, then tap and hold the page you'd like to move and you can move it around.  Also, you can add, remove or rotate the page as well by tapping and releasing the thumbnail.