Yeah I had an issue with my wasteboard not being level as well when i started. There is a forum topic somewhere on here that shows you what to do in Carbide create to plane the top surface of your wasteboard.
If you are using the ballmill as your primary tool you will have to increase your max depth of cut more than if you use the square end mill. Thats one reason the square end mill ends up being better for most of the cut operation. With the square end mill you can increase the max depth of cut slightly thicker than your stock thickness and the should cleanly cut right through.
Yes your right with the 3 job files. All you do is load the first job file and jog the cutter to zero your x, y, and z. When the first job file completes you just load the second file and click run right away. You can change your cutting bit before or after, doesn't matter. Carbide motion remembers where the x, y, and z were zeroed, so you don't need to do it again for the following job files. you can even turn the nomad off and it will still be zeroed to where you last had it. Each job file has the same x, y, and z position so just zero the first job file.
Hope that makes sense.