Yes, it's annoying having to keep 2 files of the same thing, just because of format compatibility. In my opinion, the best thing to do is to have 1 file with the best compatibility.
I won't be the first to tell you that Quicktime isn't the best at exporting to these formats - there's no configuration and the quality isn't the best.
In my opinion, what you need is
Visual Hub. There's a setting that will offer cross compatibility with all iPods, iPhones, and Apple TV. You'll also be able to batch convert and play more with the settings. But if you aren't familiar with the settings, just drag your files in, check 'iPod all' setting, push quality slider to full, and away you go. Bye Bye avi files
It's not free (about the same price as Quicktime Pro that you are using now) but there's a trial. Good luck