I haven't used it personally, but from what I read it looks like you need to:
Dump the romfs and exe folders from a decrypted oras .3ds/.cia
Place them both into a folder
Then drag and drop the folder containing both the romfs and exe folders onto the open pk3DS application
Make the changes/randomizations you want
Then repack your romfs and exe as a .3ds
And then optionally convert it into a .cia if you're using cfw.