Can you do ''layovers''? l mean, ok im flying to New York from Los Angeles, with stops in Denver, Chicago, and Nashville, is that possible all in 1 IFR plan?...without having to go back to the main screen

Just like filing a real IFR plan, you have to refile after each leg. What you can do is file each leg and save those flight plans ahead of. Then as you progress through your flights, you can just open each flight plan rather than creating a new flight plan.

What Dennis says is incorrect, a ''through clearance'' allows for multiple stops. (in the real world).