So you guys setup a separate account or something for two instances of Steam? It works fine for me albeit with a performance hit (but my rig is old) and though I haven't tried TF2 everything else on Orange Box runs, whether original engine or Source. (screenie below)
The problem I had was after fussing trying to symlink the Windows Steam install (it was before I declared mounts in fstab and depended on automount) I just copied it and something screwed up. I lost a bunch of saved games after a major download from Steam. Anybody else had that?