It's probably just as well that the thrift shop speaker didn't work. It probably would have just messed up your mixes anyway.
Those inexpensive subwoofers are notoriously loose with their definition of "sub-bass". My wife had one to augment her laptop powered speakers, and it was awful. A peak at around 120 Hz, then dropped off rapidly with essentially no response below about 90 Hz. Worse than inadequate, it made music sound worse than when it was disengaged. A friend had a more expensive one (Bose) that looked an awful lot like my wife's sub, and sounded almost as bad. You just can't get low frequencies out of a small speaker enclosure - it's non-negotiable physics. Such speakers are only going to misrepresent what's in your mix, and mess up your mixes.
Before you go looking for another bargain subwoofer, start by defining your needs. Determine where the frequency response of your Yamaha speakers drops off. You can do it scientifically with a sinewave or white noise generator and a microphone, or you can just ballpark it by ear. Either way, what you're looking for is a subwoofer that can take over where your main speakers wimp out.
This is actually surprisingly difficult to do, though, if you have no way of adjusting the upper frequency of the sub. You will likely end up with either a gap between the sub's highest frequency and the main speakers' lowest frequency, or you will have an overlap. Either way, it's sure to mess up your mixes.
The best solution is to use a crossover. It can be a separate unit, either passive or active, or built in to the subwoofer. Typically the crossover is passive and built in to the subwoofer. You then plug your main speaker connections into the sub, which then has a pair of outputs that go to your main speakers. This assures that the sub and mains smoothly merge their respective frequency responses.
If the sub has that feature, then you only have to ascertain that it can go high enough in frequency to reach the lower limit of your mains. And, of course, that it's reasonably flat across its range. Subs that satisfy these requirements can be had for between $400 and $1500. Ouch. A little more than your $15 thrift shop find.
However, you can pick up used home theater subwoofers for far less. It's tricky, but sometimes these can be made to work. Avoid the ones with down-facing speakers, and make sure they have an adjustment on the back for setting the upper frequency limit.
But even if you go out and buy a $1000 sub designed specifically for studio applications, you're still not out of the woods. Those new frequencies you hadn't been hearing before are now going to cause all kinds of problems with room resonances. Windows, doors, knickknacks and things hanging on walls will buzz. Certain bass notes will be way louder than they're supposed to be while others will disappear. It will almost certainly mess up your mixes.
A sub requires an acoustically-treated room, or at least a room designed for audio.Where you place the sub is crucial, and the best spot acoustically may not be the most convenient location. It's a rat's nest of complications. Not insurmountable problems, but it is a complicated process. You have to measure and experiment to get it right. Anything less will only mess up your mixes.
So you see, it's probably just as well the thrift-store sub didn't work. It was only going to mess up your mixes anyway.