Rodm717,
Stuart is right, turn off G28 when you post the code.
Fusion Posts the Code to make the Z go to Machine 0 for clearance purposes at the beginning of the program, every tool change, and at the end of the program.
Turning off G28 makes the Z Retract plane for your machining operation the Z end point for tool changes and/or the end of program Z move.
Also, you have to set up a Work Offset, otherwise your machine has no idea where to cut. Like Stuart said, wherever you're setting up your WCS in Fusion is where you need to set your Work Offset on your machine.
G54 is the default so that is what you set your X,Y, and Z 0.00 to.