I think memorizing sample sentences will help. PLACE: 「家の中で遊ぶ」 play AT home 「日本で生まれる」 be born IN Japan WAY, TOOL, MATERIAL: 「木と紙でできた家」a house made OF paper and wood 「ペンで書く」 write WITH a pen REASON, CAUSE: 「かぜで休む」 be absent BECAUSE OF a cold 「火事ですべてを失う」lose everything FROM a fire. I can imagine how hard it is for you to learn them because similarly it is very hard for us to remember how to use English prepositions.

"at", "by", "with", "and" etc. etc. If you're using it to say "and", pretend to write a whole sentence ending with です and drop the す, then go on with your next point/idea. When saying "at", all you do is say 'place' で 'action/topic/object etc. (whatever you are trying to express' Subject は place で time に adjective い/な verb/action を verb. That's a pretty basic skeleton that you can use for a sentence structure.

They are not hard to remember at all. I know that's blunt, but it really isn't hard. http://www.guidetojapanese.org/learn/grammar