Ya, $50 is the problem. The amp likely has a variable gain temp protection, so when it overheats, it automatically turns down the gain.
You are likely running the amp at 2 ohms, and its more than likely not supposed to run at below 4 ohms. When you hook two 4 ohm subs in parallel, the amps sees a 2 ohm load. If you hook them in series the amp would see 8 ohms.
You say you don't get enough bass when the subs are hooked up separately, so likely, you don't have enough power coming from the amp running at the recommended ohm level.
The lower the ohm number, the more the output. Literally, halve the number and you'll double the output. However, the lower the number, the closer it is to a dead short. So, a dead short is 0 ohms. 2 ohms is allowing too much current to flow in your amp, causing it to overheat.
Buy a used brand name amp that works and you'll likely be happy.