I use to have a clipboard sheet that would go on the kneeboard for FS2002/FS2004 and CFS2. it stated some rough guidelines for cowl flap usage.

here is a site that gives a good explanation of what the cowl flaps do and usage.

http://stoenworks.com/Tutorials/Cowl%20Flaps%20%26%20Engine%20C.html

from what i remember most of the time in combat aircraft the flaps would be closed for performance reasons. but at different speeds and or altitude(and temp enviroments) you would open them to help cool the engine.

Planes like the FW-190 had a fan behind the prop to help with engine cooling so cowl flaps weren't as important. American and Japanese had thier own usage.

thats all i can remember. give the site a once over as it pertains to all aircraft not just the old CFS ones that i fly
Hope it helps.

For most GA twins, having them open for takeoff and closed for cruise/descent/landing works fine.  Depending on the ouside air temp, this should keep the CHT's in the green.