I got malaria being there. It felt like a very strong cold, with fiever, coffing, stomach sick... and al the typical symptoms of a bad cold. There is really not a lot you can do about it, exept spay your room every day with insecticida that you can buy locally in Maiduguri. Now, once you have the symtoms it is very important to go to a doctor. (wont find a big hospital there, just some houses with a guy that says to be a doctor and with drugs they can give you). Drugs for malaria a pretty cheap, I think I payed like 2000 naira and got lots of different pills that got me back on my feet in 3 days.
Maiduguri is a pretty safe place and personally I never got into any problem at all that I thought I might be in danger because of being white (despite of a lot of "Osama Bin Laden" stickers on cars). On the contrary people always where very kind to me and willing to help me. (Of course you have to watch not being overpriced, I mean it´s still Nigeria, right ? :D ).
If you ever get to Maiduguri, it will probably be after being in Lagos. I can tell you this: compared to Lagos, there is absoulutly nothing to do in Maiduguri, but there is nothing to be afraid of either.