In reply to:

Since "small" mode cuts the frequencies below 90hz off, is that where I should set the EP350 crossover?

First, the x-over doesn't cut-off, it rolls-off, so your speakers will still be getting a signal below 90hz, just not as much. Second, if you're using the receiver's x-over, you don't want to use the sub's x-over, so either turn it off if possible, or set it as high as possible to get it out of the way. You don't want both the sub and receiver x-overs active at 90hz.