We've actually played this once, combing the two games. It was fun for me, visually entertaining and I wouldn't mind doing it again. Not sure there's enough to make a complete write-up, but it went something like this:
Desert could attach to fields and the roads could attach to each other. Desert cities and French cities could not mix.
When you played a tile, if possible you attached Desert to Desert and French to French. If no legal move was available that way, then you could place your tile where ever desired (following normal placement rules, of course). This was to avoid a visually obnoxious checkerboarding.
For final scoring, the Wolf could travel through Farms to eat Sheep. Aside from that, Deserts and Farms were not considered attached for Farmer and Shepherd scoring. A Farm did score points for a Desert City if it was no more than one Desert tile away.
Roads were Roads, only one Thief/Pilgrim (as we call the AotC road followers) per Road, no matter its composition.
Because the Desert Fields were more fragmented than usual by the French Farms, the Shepherds didn't score very well. Farms did all right, probably because 1) they could feed Desert Cities and 2) there were more French tiles in the game.
We used AotC and LE Carc -- Carcassonne with I&C and T&B expansions plus Tower tiles (no towers, though). I'd do it again.
Only next time, I want to include the Dragon just to see what happens when the Dragon and the Ark meet... something horrible, I'm sure.