Phase A & B measurement accuracy using Halscope

I'm in the process of putting together another CNC lathe using a Grizzly 10 x 22 G0602 and was planning on making my own encoder disk. The size of the lathe will allow me to make a disk with 360 slots where I'll have 1 slot cut for the index pulse and the remaining slots will be used for the A & B spindle phase inputs using separate optical sensors.

My question is whether or not halscope is accurate enough to use to adjust the 90 phase difference between A & B spindle phase inputs. If not I'll have to find a scope to get them set properly. Has anyone done this before?

Thanks

Is there a tutorial for running Halscope in the base thread or is base thread the normal mode for Halscope when you start it up? I've used halscope before but never payed any attention to whether or not I was using it in Base thread. I'm going to guess the base thread is the real time sample period with no multipliers? This would normally read slow when the dialog box first show up?