Hi Paul!
I use a large CMI Large Ultrascender for my upper ascender and it contains two holes at the bottom of the ascender body. One hole is dedicated for my footloop, which will go through one of the rollers in my chest box. The other hole I attach cordage that goes to my sit harness. When I climb, the cordage attached to my sit harness is NOT included in the roller. Actually, it runs pretty smoothly next to the roller that the corresponding footloop is in. I understand that this technique may not work for everyone, but it's served me well the last few years. One reason I think it works so well is that that cordage connecting me to my sit harness is a bit thinner than the one used for the footloop--not ideal, but works great for me.
For peace of mind, if you can't find a way to attach the upper ascender to your sit harness, I'd clip the Croll onto the rope and let it ride up w/ you, especially on longer drops. Since you already have included it into your system, if it run smoothly, it seems silly not to use it.