My workflow for dealing with cloth simulations is to give myself about 15 frames before my actual animation starts where I go from default character pose to their starting pose so that the clothes can start in a non-intersecting state and properly deform around the character. I do this with 3ds Max’s cloth plugin and Maya’s ncloth.
Does anybody do it a different way? This is the way that makes sense to me, but it seems hack-ish.