I am using cut 2-D and have a router CNC operating with homing limit switches on one end and using max limits on the 4th input as well as soft limits, I have just been doing basic cut outs with flat head end mills thus far. I would like to start adding detailed cuts to my parts such as bevels but am unsure of how to handle the tool change. Because of the limit switches I know I cannot use auto-zero.

 How can I do this manually if my tools are different length? Do I adjust when the machine pauses and requests a tool change by moving the machine off of the part, change the tool, bring it back over the part and touch off to the surface and re-zero the Z only?

I have looked for steps and detailed guides on how to do this but I am unsure and really do not want to damage anything.

-Silent

You can wire all your home switches to one pin, and home each axis consecutively, to free up a pin for auto zero.

Otherwise yes, you jog back over and rezero the Z, then continue.