Looks great in there, and nice touches on the wiring too.
Gotta trade some form for function, but it must be a pain to tune that amp installed like that, but it certainly looks better where it is. Once it's tuned you shouldn't have to touch it again.
For the tuning, I would start with getting the sub blended in output wise by adjusting the gain by ear to where it sounds right.
Then I would leave the "infrasonic" filter off, only really needed on a ported box, or a large sealed. If you hear the sub bottoming out, or sounding slopping with really deep notes, you could flip this on to see if that clears it up.
For the "Freq hrz" knob I would start about half way up (around 100hz) and then slowly work it down to you liking, or maybe turn it up (always in small increments) to see if it helps fill in where the mid range speakers are lacking.
Tuning can be tricky mostly in a patience sense, but its nice when you finally get it dialed in. You want to make small changes, then listen, then small changes, and listen, and you don't want to change more than 1 aspect at a time either.
Looks good but you should have the fuse under the hood as close to the battery as possibly. The main reason for it is in-case the power wire were to somehow ground out, the fuse will blow and keep from shorting everything out. With having it by the amp, the only thing you are saving is the amp. Just my 2c
Yup!! I forgot earlier, this amp actually doesn't have any internal fuses. So there is a fuse holder up under the hood (the one he said that the clips broke on) and then the fuse pictures above the amp. Sucks having to run a pair of external fuses like this, but better safe than sorry, 1 under the hood to protect the truck from burning up, and one by the amp to protect the amp.