This is an interesting H-A-D posting of a FREE circuit simulation program. Worth taking a look at ...Tiger http://hackaday.com/2015/07/20/a-breadboard-in-a-browser/
When you say "layout" do you mean a circuit board? This doesn't do pcb's. This also couldn't simulate an entire flight controller. You might be able to simulate it a section at a time. Not really the right tool. ...Tiger