The Monoprice Encore speakers would be much superior to those speakers. The Klipsch sub would have more output in bass than the Monoprice speakers, but the Monoprice Encore speakers would probably have better sounding bass. The Sony STR receiver isn't going to be very sophisticated with subwoofer integration, and my guess is that you don't want to spring for a complicated microphone measurement system, so I would skip any single sub system when you could get the Monoprice speakers.
If you wanted to do something a little fun and crazy, you might try this: get two of
these Dayton 12" subs and a pair of some
Encore bookshelf speakers. Use the subs as speaker stands for the Encores. That should act like some tower speakers with a formidable bass section. If you really want to have some fun, swap out the Encore bookshelf speakers and use
their center speakers but oriented vertically- that way you would still have the headroom of the tower speakers but a more powerful bass section. If you want to go super bonkers, spring for a couple of the
Dayton 15"s over the 12"s.
Keep in mind that I would only advise getting subs over the Encore towers if you are able to get two subs. Like I said, you don't have much hope of integrating a single subwoofer well into a system within your budget and your AVR. But if you go with dual subs and locate each with a standmount speaker, they act like tower speakers, and integrating the subs will be a lot easier to achieve a good sound.