So I have the bitsetter and touch probe too. Both are hooked up. Earlier today I went to start a job. I zero’d z axis with bitsetter after initializing machine. I then went to zero the x and y axis with touch probe. Since I didn’t want to zero the z axis since i did that with the bitsetter, i went to do the x and y axis seperate. Once I went to zero the y axis though in front left corner, the probe went to the right which made no sense to me and it gave me some error. Next time around I did all axis’s with the touch probe and it zero’d properly
If I’m understanding you correctly, I think the issue is that the BitSetter doesn’t actually “zero” anything, it just calculates an offset from an existing zero. So in other words, you have to zero using the touch probe (or paper, or whatever) first, and then use the BitSetter. Julien’s most excellent book has a section on this which explains it better:
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And re-reading that short section I wrote (and that other section about the workflow for a multi-tool job), I realize I should highlight more clearly how the zeroing with the touch probe and the tool length offset are two different but complementary things. As @RickT said, the BitSetter “only” serves the purpose of figuring out the endmill length sticking out of the collet (and its variation after changing endmills), while the probe “only” serves the purpose of defining an absolute X/Y/Z reference point in space for toolpaths (zeroing).
Another way to see this is, the (fixed) Z height of the BitSetter pushbutton is different from the (variable) height of the surface of your stock for a given job, so there is no way just using the BitSetter alone could establish a correct Z0 associated to your specific stock/job.
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Thanks! That makes sense. I understand now 
Thanks Rick! I appreciate your help
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