Without any pictures or anything else to go with, trying to find this answer is finding a needle in a haystack.
Luckily for you, I also have a 4 channel amp with the FARK so I'm going to try my best here.
The problem with the FARK and a 4 channel amp, if you hook everything up directly, then you have no signal going to the subs. If you got the full kit, then you received two harnesses, the X3 harness and the X2 harness.
The X3 harness is what connects the stock headunit output into the RCAs:
The X2 harness is what connects your amp to the stock speaker wires:
So let's start from the stock wires and work our way around. I'm assuming you connected the X3 connector which has the RCAs plus an orange wire. You connect your RCAs from the X3 to your amp and you run a remote wire from your amp to the orange wire on the X3 harness. Now your amp has signal. This is all assuming you powered your amp with a positive wire (with appropriate fuse) and ground wire.
Now let's switch to the X2 harness. If you have this harness, and you've attached it to your 4 channel amp, then you have properly amped the rear deck speakers and your door speakers and have no signal running to your sub set up.
Now I believe your JL 400/4 amp should have 6 RCA attachments. 4 input and 2 output. If this is the case, then you should be running a 3rd pair of RCA cables from the JL 400/4 amp output RCAs to the MTX input RCAs. Something like this:
Hopefully this helped. But please provide a little bit more info so we may help you better.