First of all setting the speakers to large generally means that it bypasses whatever crossover you're setting. So if you set the front three speakers to large you're running them full range with zero crossover. If your surround channels are set to small then they are they only thing delivering a signal to the subwoofer, hence why it sounds weak. (I admit I haven't looked at the manual for the Yammy to know for sure)
Setting the speakers to large won't necessarily put too much strain on the receiver, as the internet also explains. It really depends on how loud you're playing and the efficiency of your speakers. As the internet also explains, since you have efficient speakers (being that they are klipsch) your receiver is more than capable of delivering loud noises to you.
If you are sitting 15 feet away and only using your front towers then you only need 50 wpc to get over 100db, not accounting for room gain either.
with a 15 ft distance and 5 speakers you're at 105 db. These are extremely loud levels and without accounting for room gain.
In other words, if you had just sold the Yamaha, gotten a better receiver with enhanced room correction and a more robust power supply and a better sub, you'd be in much better shape. The money you spent on the XPA-3 is kind of a waste when your subwoofer and receiver could have been improved with more noticeable audio quality improvements.
Of course we all like to get new things and improve our gear, but at your stage in the game and with your equipment, you're improving the wrong part. You improved one of the pieces least likely to improve SQ. A new subwoofer or a better receiver would have been a better buy.
I don't get your logic. There are pieces that have been recommend that would yield immediate sonic improvement and yet you still bought the amp? You won't gain any sonic improvement from the amp, especially because you have speakers that are made to be very sensitive and not need a lot of power. You'll run into thermal compression long before the yamaha runs out of power, and far far far far far before the XPA-3 even breaks a sweat.
If you're dead set on just spending money to spend it, that's ok to each his own, but to use your own example, if you're not going to listen to good sense when you're on here why come on here for help?
Just sayin' Don't misunderstand me, I don't mean to sound like a total a$$ but I'm trying to tell you that adding an external amp shouldn't be the number one thing on your priority list if you want to upgrade something at this point, unless you just want something that's going to sit on a shelf and look cool.