Something like DiskAid seems the way to go for moving sets of files over, but if you use Dropbox, you can navigate to a file in Dropbox on your iPad, then tap Open In... and select Pythonista. This brings the file into Pythonista and seems to place it in a special folder named Inbox.
From there, you can move the files to where you want them.
PS: Thanks cminton for the pointer to nflgame - looks sweet.