Ok well first of all, i think u mentioned it wrong in the beginning. It's a MTX Thunder 152 AMP, not sub correct? Well it should be.
To answer the first problem: "1.) The amp runs very hot. I have it hooked up by parallel. " Don't worry about it. Amps will get hot to extremely hot. It's because you're drawing a lot of wattage from it and to put it in terms that's easier to understand. Does your tv get hot when left on? Just look at it like that. Like most amps, your amp has a "automatic" shut off when it reaches a specific core temp. When that does happen, it doesn't necessary mean that it blew, it just needs time to cool down. And with that in mind, it means that u need more flow of air to cool it down so u have to relocate it.
To answer the second problem: "2.) The subs seem to distort, almost sounds like its farting, and I'm not even playing it that loud. Its like they sound like they are going to blow, and they vibrate a lot. " From what the specs show, your subs should handle what your amp pushes. I mean your subs at RMS is 150W at 4 ohms. So when you bridge them u're running it at 2 ohms. From what your amp specs reads it says 75W x2 at the 2 ohms load. So from that I would have to say that your amp is too weak to power the subs but it doesn't mean anything. In other words i'm trying to say that you're running everything in "Safe mode".
You say that your subs are making a farting noise. I'd have to suspect it being blown. Even tho everything's safe, there could've been a tear or something in the sub. I would also have to look into the enclosure. Someone recently posted that they've been hearing a farting noise lately and concluded that it was the enclosure.
About the bass being affected when changing the HU outputs. It's gonna happen. Because you hooked ur amp to the HU, it's like everythings running in parelle. One thing get affected, everything gets affected. Having a HU that has sub outputs will change that. Even having a EQ for the inside spkrs can change it.
Well i'm getting tired. Someone please write!