Hi Bobby,
No, don’t use the 2.5D
Under Config / Ports & Pins / Spindle setup, specify an Output # for M3 (1 would be good). Then under Output Signals for Output #1 specify the port and pin you will be using to drive your pen up / down.
Then the GCode M3 / M5 will activate / deactivate this pin accordingly.
If it is any help, you can e-mail me or post here a sample copy of the code you are planning to use and I will check out the compatibility etc.
Tweakie.