Hi Clayton,
You don't need to use the C Programs Screen to Initialize your system. Instead assign a User Button in KMotionCNC to run it.
You also don't need and probably don't want to initialize the system all the time. You should just do that once at the beginning of the day.
I'm not exactly sure what you man by:
Does that mean you Jog the tool tip to some reference point?Zero tool (1) at 0,0,0
It seems you are moving to a fixed tool change position with: G0 X0 Y0 Z6. This may not be a good idea because the position will depend on how the system was last "zeroed" You might want to use G53 to move to a fixed machine position so it won't matter where/how the system was "zeroed".
There are many ways to do things but one way might be to:
#1 Initialize/Home only at the beginning of the day
#2 Move to Tool Change Position and load Tool #1
#3 Jog tool to reference point then Zero all. DROs should always read exactly zero
#4 Load/run File #1
#5 Move to Tool Change Position and load Tool #2
#6 Jog tool to reference point then Zero all. DROs should always read exactly zero
#7 Load/run File #2
HTH
Regards