The London School of Tropical Medicine have a very helpful information department and are more useful than, say, travel clinics when it comes to advice regarding long-term usage and risks of anti-malarials. I'd imagine that their links with the military will mean that they have dealt with pilots many times.
As for the duration of use for the medicines, this info is being updated on a regular basis as more gets known about the newer drugs. Mefloquine (Larium) for example used to be limited to something like 3months but can now be taken for much longer as it has been around long enough to gather more data. Having said that, pilots are not supposed to use it.
Without teaching folks to suck eggs.....Best advice is to check what the local drug resistance is (from a reputable source). Find a non-resistant drug and check with Aviation Med specialist that is ok to take when flying. If you have a specific drug in mind I can probably find out how long you can take it for (email the drug name to me) - but I can't comment on suitability for flying.
And cover up!
PB