Learning the acupuncture points and related theories can certainly be an overwhelming amount of information to digest and recall. Personally I found that drawing the meridians out completely on paper with their locations and one or two basic usages - over and over - was the most helpful way for me. I used to do a meridian nearly every day. The exams were usually quite easy at that point with so much repetition. I also built parts of this site when I was in school and used the "mouse overs" on the meridian pictures to help quiz myself. So if you go to any meridian page, say the Large Intestine, you can hold the mouse over a particular point and the location will appear on the page (it works better in a web browser like firefox than in Internet Explorer as IE seems to show only a certain number of characters). This way you can go down the meridian and see if you can remember the locations.
As for the theories themselves, yes they are confusing. And, like many philosophical constructs, they don't always make complete sense when you try to tie everything together. The theories are simply pointers to phenomena that exist in our day to day lives. For me, applying the theories to day to day subjects or conditions was always more helpful than thinking of them in the abstract. If the theories have no deeper meaning for you, it's hard to remember them. For better or for worse, many schools start off teaching all the points and theories completely detached from their clinical usage and this seems to make it more difficult for some people who understand more deeply when something is applied.
Generally, though, I wouldn't worry about a thing. Just do your best. As you go through school everything will start to fit together more and more and at some point the foreign or mystical nature of some of the theories will disappear and much of it will seem just like common sense to you at that point.
I wish you all the best in your studies and encourage you to use the forums, etc. to help you work through issues that come up during your schooling and beyond.