Yes, leave on through. The acoustimass, not sure which version you have of the 10 series, are designed for a full range signal to be sent to the module as it handles the crossovers for the various channels. So, make sure the main channels are set to LARGE in the Yamaha if YPAO didn’t do it from the get go. I’d assign the ceiling speakers as OVERHEAD, not FRONT PRESENCE in the Yamaha. Set them to SMALL with a crossover of 100-110 and see how it sounds. Enjoy! Oh, and welcome to the forums.