It shouldn't really matter in theory, as the sim is for you to learn and to practice the principles behind instrument flying and nav - it's not to teach you aircraft handling.
However, it is such a brainache learning these things that any advantage you can get to make life easier is a bonus, and having a sim representative of the a/c you will fly is a big plus. If your going to fly the Seneca, try and use a sim with a seneca layout. It will just help to ease the pressure a little bit.