It seems like when you take something apart you always think that you're gonna know how to put it back together but then time passes and it's not so clear anymore. Anyways, I am installing the headliner molding that goes along the roofrail on the sides. On each molding it has one side that it longer than the other. My question is, does the longer side face the inside of the car or the outside?

I believe you are refering to the windlace. The side that has an extra sealing surface goes to the outside, the thinner side is the inside.