I would be very wary of this. Using an iPad as digital textbooks is a fine idea, especially because you can mark them up, which you can't really do on schools books. And being able to store files I guess is cool, and if you want you can take notes right on the ipad, although the handwriting recognition isn't spectacular. If you really want to take the time to write on paper and scan, then that's your decision, but a pretty good one. It's time consuming, but will be very easy to organize all of your notes.
If I were in your situation, I would do all of my work on whatever format the teacher sends out. If it's a handout, then just write on that. If you're handing in a paper and the teacher says "please print it out," then print it out. If they're fine with you sending them a word doc, then great for the teacher for modernizing. Commenting on papers on the computer is really easy, as a lot of college profs have already discovered, and HS teachers can do it easily too. But keep it in a word format, not PDF.
I would just have the iPad, and say a 1 inch binder with the paper assignments that I need to keep around, and as soon as I'm done with them, remove them from the binder to keep from getting heavy. That's just what I'd do.