stereochemistry is definitely a notoriously tough subject for many ppl in orgo. so don't feel bad. it takes a while....it really does help to get a model kit and build the structures. as far for the rest of the course (and the mcat) it is important to understand enantiomers/diastereomers (esp cis trans), assigning priorities, chiral centers, etc. but don't sweat it too much - as long as you can recognize mirror images and decide when a reaction has the opportunity to produce a mix of products (i.e. look for a chiral center in the reactant), you should be ok. right now, focus on really gaining an understanding of sn1/sn2/e1/e2 reactions, because these mechanisms will come back to haunt you later on. i.e. understand what makes a good nucleophile and leaving group, the effect of sterics in forcing sn2, carbocation stability, etc. especially understand the pushing of electrons and arrows...this will be a needed skill when you get to reactions of alcohols and carbonyl groups. i know it seems overwhelming right now, but if you plug away at it and really understand it now, you will be all set for the rest of the course.
what textbook are you using? i'd recommend getting wade, both the textbook and soln manual, working all the problems and reading the sections. it made things crystal clear for me.
good luck and feel free to pm me if you have any specific orgo questions 🙂