Since you have a sub, you want to set the RTi12's to Small. I believe they go down to about 40 Hz so you can use 60 Hz or 80 Hz as a crossover. If you really want extra bass you can set the RTi's to Large and set the 'double bass' option on the receiver to on.
The sub's xover should be set as high as it will go since you will be using the receiver to do the bass managment. Some subs have a dedicated input that bypasses the sub's internal xover (often labeled 'LFE') and if your sub has one then use it for the connection to the receiver - in that case the position of the sub's xover dial is irrelevant because it will be bypassed.