You may want to consider making two Smart Playlists based on bitrates, one for ALAC and the other for AIFF. Here's how:
For ALAC files:
1. Click File >> New Smart Playlist
2. Check 'Match the Following Rule'
3. 'Bitrate' 'is less than' '1411' kbps
4. Check 'Live Updating'
5. Click OK
6. You'll now have a new playlist called 'untitled playlist'. Rename this to something appropriate (eg ALAC Files).
For AIFF files:
1. Click File >> New Smart Playlist
2. Check 'Match the Following Rule'
3. 'Bitrate' 'is more than' '1410' kbps
4. Check 'Live Updating'
5. Click OK
6. You'll now have a new playlist called 'untitled playlist'. Rename this to something appropriate (eg AIFF Files).
Select the AIFF playlist for playback, and the ALAC playlist for syncing.
Another option is two create two separate libraries. One way is:
1. Convert your files to AIFF using a program other than iTunes (like Max, making sure to store them in a different location other than the iTunes library)
2. Create a new library in iTunes (start iTunes while holding down the Option key)
3. Add the converted files to the new library (File >> Add to Library).
This option, which may seem more convenient, requires more maintenance as you'll have to do an outboard conversion, switch libraries, and then add to library each time you rip new music (or, alternatively, rip the music for each library separately). The playlist option takes care of 'separating' the files itself.