Picking up noises

No, not the cables.

You made a switch in head units and the noise started.  That's where the problem is.

Of course you need to amplify the subwoofer, so connecting subs directly to the deck is no solution.  You have a problem with grounding, and the Pioneer deck is the culprit.  It may be defective or you may have to ground it differently than what is being used now.  The ground from the deck to chassis must be on the same page as the ground from the amplifier to chassis.  A difference in the ground planes between the two components is causing a ground loop in your sound system.  Work on running a separate ground wire from the deck to the car's chassis.  If the problem can't be solved look into replacing the deck with another one, because the deck itself may have ground plane differences in itself.

And read through forbidden's grounding topics stickied toward the top of the page for a clearer outlook of this problem.

"My amp is connected to the fuse box as well."

That statement bothers me....why isn't the amp connected directly to the battery? 

Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.