Your first step in understanding them will be to stop equating them to = in, at, on, to etc. This will only confuse you. And I will just tell you now that its tough to directly translate a lot of English and Japanese, so you need to learn to think in Japanese, and not depend too much on what is the exact translation of this in English.
Read lots of simple sentences with the particles in it, and try to memorized some set phrases. Grapefruit explained the meanings quite well so I have nothing to add there. Bottom line is mastery of prep particles is hard. It is best just to get the basics down and continue to increase your vocab, and learn to say other things. It will come in time, you will develop a sense about them. Maybe not like a native speaker, but you will eventually gain intuition as to what the right particle is for each situation. Good luck.