Hey Tim,
I may not completely understand your question, but, why don't you complete the pocket in one pass?
If I want to cut a pocket thats 1 inch deep with a 1/4 inch end mill, the tool will only cut to the depth of your setting....(mine is set at half the diameter of the tool)...it will make a .125 pass then go to the next depth of .25 and so on till it reaches a total depth of 1 inch.
This is all in one toolpath and is visible by the preview as multiple lines cutting to your max depth.
The tool should cut this in one operation unless you are running multiple toolpaths in the same file, in which, it will return to safe z after each completion and then go to the next gcode file.
Chuck
Aspire, VCPro, PhotoVCarve, Cut3D, Mach3, Home built CnC.