I never downtune so I've never had to deal with this but I would think that dealing with it would be like if you were changing string gauge. Downtuning will most likely screw up the balance of tension between the strings and the tremolo springs. You should probably tune down and then take a look at the base plate and see whether or not it's sitting parallel with the body of your guitar. If it's not (and if you're downtuning it'll be tilting towards the body), then open up the back of your guitar where the tremolo springs are, look for the two screws that hold the plate which the springs are connected to, and loosen them just a bit (turn them counterclockwise). Only do about a quarter of a turn though. Then retune to whatever tuning you want the guitar to be at (adjusting the springs will put your guitar out of tune), look at the base plate again and if it's sitting parallel with the body then you're done. If it's not then you'll need to adjust the tremolo springs again. As far as I can tell this is the only kind of problem you'll have with downtuning. You just need to balance out the tension between the strings and the tremolo springs.