I started planning all the dimensions for my plane in meters, and another question popped into my head. . .
Are windows done in the model itself or while painting :question
You're asking all the little questions. Start working with the modeling program a bit, and then come back and ask questions like that.
But to answer a couple of your queries:
You don't need to rescale anything. The modeling program will scale things for you. It programs itself in either meters or feet and you decide how big you want it to be in the sim, and make it that big in the modeling program.
The SDK is NOT a modeling program. It just contains usefull info and resources, plus a couple of tools necessary to make a model. Gmax is a modeling program, and the only free one available for direct conversion to FS.
Windows are at your discretion. Some people opt to model the windows directly into the 3D model. Others make them using a painting system. Generally, the AI specific aircraft will have them painted on, while the flyable aircraft will have them built in. This is not a rule, however. The smaller aircraft (Cessnas and the like) are always modeled with the windows. Most jetliners, or anything larger than a business jet, can be made with the windows not modeled in. It's truly at the designer's discretion.
Now: GO GET TUTORIALS! COME BACK WHEN YOU'VE READ THEM!
