I play mine in concert - the usual "spanish" tuning, and I find that the MOST important thing is to make sure the unison pairs are unison and the octave pairs are octaves.

Trying to get individual string compensation on the saddle is going to be a nightmare, but it would be good since otherwise end effect takes teh fatter strings sharp faster thanthe thin ones as you go up the neck.

The other idea is to keep a capo JUST for the 12 string, and groove the rubber so it stretches the fat strings not so much as otherwise they are pushed harder by the capo precisely because they are fatter.