As others have already pointed out, Flying J locations have RV specific facilities, not Pilot. Hopefully now that they've merged, they will continue to build RV friendly facilities.
We haven't done any overnight stops since we bought the travel traile, but we used to in the motorhome. We only stayed overnight at Flying J a few times. We usually found quieter/better alternatives. We do however look for RV friendly gas lanes when towing the trailer. I try to always fill the truck up when we're disconnected before the day starts but even at that I have a limited range and usually have to fill up somewhere on the road with trailer in tow.
On our recent trip through NC, Va, and TN, we found most Sheetz locations to be adequately sized and layed out such that we could get in and out reasonably even though they don't have dedicated RV facilities. We only saw a few Flying J locations on our route. Other brands including many of the truck stops and "travel centers" gas lanes were very inconsistent.