Hey Dawn,
if you have a tool change event (M6) in your program, the factory settings of Onefinity Controller let the machine simply stop and emit a message. It does not lift Z in order to allow you to change the tool or to probe Z then. The solution for Onefinity Manufacturer is not to have tool changes in your program (period).
The Onefinity Controller is a fork of buildbotics.com Controller. You might be interested in what the creators of Buildbotics Controller suggest that CNC builders and owners instead let the machine do at ‘tool-change’ event, in order to be able to change the tool, as is explained here.
Unfortunately jogging around during tool-change event is not yet supported. But the example linked above allows a nice tool change at a position of your choice and a Z probing (necessary for the machine the know the new tool length).
A touch probe is highly to recommend in every case!