Yes, prepositions are a notoriously tricky area of English grammar.
Lots of reading will certainly help, because it will expose you to prepositions in context. And when you're reading academic texts, you will encounter prepositions that occur with academic phrases and terminology (for example,
an analysis of; an investigation into).
So, one way of learning prepositions is to learn them in conjunction with the words they occur with (for example,
in conjunction with; occur with). So when you learn a new word, make a note of the preposition(s) it takes.
You can also organise your grammar/vocabulary notes around these prepositions, by storing words that take
into, words that take
with etc. You can then use these notes to refresh your memory or to test yourself.
You might then like to make recordings of the word patterns (on your iPod/mp3player/mobile phone), or you may prefer to use pictures to help you visualise the prepositions. Some people use small cards with words on one side and the prepositions on the reverse side to test themselves.
These are just my thoughts - does anyone have any other ideas to add?
Cheers!
Martin