I was wondering if it was possible to use the peptide building tools with protected amino acids?  I have several protein structures with benzyl-protected glutamic acid.  Would it be possible to add new amino acids to the protein building tools?

At the moment, no but that's a good idea. On the other hand, in Avogadro 1.1, it's fairly easy to add the benzyl groups to the side-chain. Select the insertion point (either the hydrogen or the oxygen atom) go to Build -> Insert -> Fragment and pick out benzene.

You should also be able to select multiple atoms and perform the insertion across all of them at once.

Hope that helps,
-Geoff