My wife has painful knees and hips, not made any better by riding pillion. Painkillers are always in the top box.
She doesn't like the back rest on the top box, it pushes her too far forward (even with the box set further back) the back protector in her jacket is enough to cushion her.
Don't accelerate or more important brake too hard, then they don't have to use their legs to stop themselves sliding forward.
Having the intercom is a bonus, she will tell me she is going to drop her legs off the pegs for a stretch or asks me to slow down for a bit so she can stand on the pegs for a bit of adjustment. (These done in sensible/safe/ quiet areas).
11/2 hours seems to be our cut off time. 10 or 15 minutes is usually enough to refresh.
When touring we stop regularly, often before the 11/2 hours to have a break/look around/coffee, etc trying not to get to the point where you 'need' to stop. Once you get to that point that 'need' time gets shorter as you go on!
It's not as much fun on the pillion so listen to their requests opinions etc. They will differ to yours! (In fact that's usual isn't it?)
Most important, never frighten them!!! Cornering too fast or 'close' overtakes etc causes sharp pains in the riders kidneys!!!