Your situation is unusual because you have a split collection. My advice would be to unify your collection. In particular:
1. Take your master library, which only has FLACs in it now and add in *only* the MP3s of the songs that you don't have as FLACs. As you do this, you should either manually, or with MC's RM&C tool, move these MP3s to a new directory. That way you know that these are your unique MP3s that you don't have FLAC copies of.
2. Now your master library will contain *all* of your songs: Some in FLAC and some in MP3.
3. Since your master library contains all of your music, you can now do a handheld sync to a *new* directory. This handheld sync should be set up to only allow MP3. That way it will copy the MP3s and convert the FLACs to MP3s.
You'll end up with a directory full of MP3s of your entire collection. You'll probably also have a redundant directory full of MP3s that are duplicates of your FLACs. You'll probably keep that around for a while until you're super duper sure that you have all of your unique MP3s copied to the master library.
This approach keeps things complete and simple. No split collection. It's all one collection. ...and it has a synced version that's been converted to MP3.
Further, your handheld definition(s) can specify playlist(s), etc to only copy what you want to the handhelds. That way you don't need an MP3 copy of the entire library. Only what you want to put on your ipod. If you want different stuff on each ipod, you can just make two handheld definitions, and each one will get what it is supposed to.
Finally, you'll need to sync these directories to the ipods. I'll leave that part to you, as it might involve itunes or a third party tool. For the one ipod I started working with recently, my first step was to RockBox it, so it just appears as a normal hard drive and doesn't require any special software to sync to it.
Good luck,
Brian.