How do you not restore from backup?

[Hopper200456]

Hey, so, I got a replacement iPad because my other one was defective. I was told by the apple employees not to restore from my back up I had. (It was corrupted or something) so, I set up my new iPad WITHOUT using iTunes on my computer. So, now, a few months later, I've got all my stuff back, and all the files I want, and what not. But when I plug it into a computer to put a song onto it iTunes recognizes it as a new iPad and wants me to:
A, Set up new iPad
B, Restore from backup (Which is corrupted.)

What should I do? Will clicking "set up as new iPad" erase all my existing data?

Thanks, -Hopper