ok im not 100% sure on this but im going off of memory. i believe that the stock woofers are rated at 6 ohms of resistance. the aftermarket speakers are rated at 4 ohms of resistance. basically the less resistance there is, the more power it will pull from the amp. however, the amp can only operate at a certain resistance (in this case 6 ohms) before it overworks itself and overheats....then the bass diminishes and either turns off and goes into protect mode or just burns itself up. so at 4 ohms, there is less resistance, speaker pulls more power from the amp, amp cant handle it, amp overheats and goes bye bye.
this is the most common scenario i see.. you can try to put your factory woofers back in and see if the amp still works, but im guessing that the aftermarkets may have burned it up.
in the mach systems, the deck runs the tweeters and an amp runs the woofers. or in some, an amp runs 2 woofers and another runs the other 2.