first of all, make sure the car runs well whatever you end up getting. if you want to know the difference between the two, there are a few. the integra is lighter, its basically a sporty version of the civic with a completely different chassis and look. the engines also had the b-series after 1990 which were DOHC compared to civics. now the reason why i say they are a sproty version of the civic is the fact that the integra has a very similar weight as the civic. the prelude is heavier and therefore needs a larger motor, but it is not much heavier than the integra, really preludes are roughly 2700 lbs for the last generation of them. these engines are the H-series, the H23 is nonvtec that had an output of 160ish hp, the H22 is the vtec version which came with 195. if you are lucky enough to come across and SH model prelude it will have either the H23 or H22 that puts out 220 hp. the integra b-series engines were relatively low in hp, with the highest hp for regular integras reaching upwards of 150-160hp in the last models. the GSR integras got around 175-180 while the integra type R got 190-195. as for parts, both cars have a very wide selection of parts and aftermarket upgrades. if you get an integra get one that is at least 1992, replacing parts are a little easier with the suspension i believe and they are easier to come by as well than integras older than 1992. other than that, its just a matter of what you buy, but remember to test drive the car and take it to a mechanic and get their opinion so that you dont end up with a broken car in the near future, since the prelude and integra are sports cars and are driven harder than pretty much every other honda/acura made.
lastly, manual would be better since it takes some weight off and you can get better gas mileage, the price of the car will be cheaper, and repairs will be cheaper. plus everyone should know how to drive a manual, its not hard at all.
