To start off then I have no experience with the Ars magica, but I believe my experience would work as a charm.
I have been playing a little with the company rules for my games, what I have done is to add positions within each company for each Quality then connect there main attributes/skills to the ability to get the "Temporary Raises" on the Qualities.
There is still question of character skills interaction with Might and a Mass Combat System, Character wealth conversion to Treasure and back and controls on that as Treasure is much much more then gold and sometimes gold is worthless as Treasure, and also how to handle the followers that help build your Sovereignty and the occupation of Territory.
here is a quote from GregStolze that helped me somewhat.
Re: Help Using REIGN's Company Rules With Other Games
The comments here seem to have things covered. The Company rules were
designed to be loosely coupled, so the only major point of interface
is "Raising the Pool." I really don't think there should be any
unexpected effects that swarm out of nowhere to bite on you. The only
problem I anticipate is that the success/failure curve in the ORE is
quite different from D20 stuff. But given the disconnect between the
circumstances (personal vs. nation-wide), the disconnect between
mechanics ("Man, we busted our humps and STILL couldn't get a set?")
may work just fine. The relative rarity of the ORE rolls (because PCs
can scurry around doing all kinds of stuff, while Companies work on
the scale of months) should, I think, make them more dramatic and
breathtaking. That's the plan, anyhow.
GregStolze, 2011-MAY-13 at forum.rpg.net