Both are the same thing (I think MP uses daily builds from master branch for SITL though. Cygwin lets you choose by checking out a version with git.) if you ware just running it without specifying a different flight dynamics simulator. By default JSBSim is used with a generalized fixed wing model. If you want to test a model of your particular aircraft, I would suggest building a model of it in one of the supported simulators and then using SITL to connect ArduPilot to the simulator. There is also the forum section for Plane Simulator where a lot of the simulation discussion happens. https://discuss.ardupilot.org/c/arduplane/plane-simulation/26