Thanks for the input @Ihoujin.
I figured it out but wanted to leave this to help others too.
This is one I've seen a great may people struggle with, and for good reason. There is more than one reticle and subsequently more than one method.
Some polar finders show a bubble to align to using the above description and the RA setting circle, once the reticle is calibrated to the correct angle as above. This was the situation on my CG4 once I bought a polar scope for it but the EQ6-r comes with one installed and the new reticle shows the hour and three concentric circles.
My question (which the title didn't say) is more related to the one shown in KSTARS polar angle calculator. Turns out the EQ6-R polar scope reticle matches this screen pretty well and I was able to set from it directly without flipping. I don't have any screen at the scope so it didn't occur to me until I questioned it. My AHA moment was realizing the numbers are already flipped to show a direct representation in reticle.
I found this in another forum but am pretty sure it't from the SW manual: "Rotate the r.a. axis of the mount to put the 0 oclock of the reticle at the highest position in the FOV of the polar scope, then place polaris at the correct clock position given by the hand controller or other device."
The synscan controller would give me the time in numbers if I had it on the unit but i'm using an ftdi cable direct to the indiserver sbc.
The 12 hour version is showing my local time on the hand, and GMT on the digital readout while the 24h reticle shows gmt in both places. Ouch... I think what confuses this is that there are at least 4 different versions, setting circle, time reticles north and south star angle estimators. and lots of different version in apps all over. It's no wonder people are confused. I think the simplest answer if you have a clock reticle is to put polaris to the spot in your reticle where the red thing is pointing... THat is unless something is flipped/notflipped in the app or reticle. People really should include a caption for that in their apps. For me the numbers line up.