How can I put an entire ROM in my submission when I clearly submitted an ips patch & readme file?
As I understand it, if you start out with, say, a 1 MB ROM, and then do some crazy expansion stuff and end up with a 4 MB ROM, and subsequently use the 1 MB ROM to generate the IPS, then yes, the IPS patch will pretty much include most of the ROM. (Of course, it won't really be in a form that is actually useable
as a ROM, but this is a rather sub-optimal result when the whole process is supposed to avoid distributing copyrighted data.)
So, yes, you may have screwed up your patch creation process. To make sure you're doing it correctly, maybe try taking a ROM, changing a single byte, and generating an IPS file. If you don't end up with something teensy-tiny, you're doing something wrong.