Hi Stuart,
Finally got my amp and sub hooked up to the standard HU. However if i have both left and right speaker inputs hooked up to the line level convertor, its sounds so bad, so with one disconnected its fine. Must have a miswire somewhere!. Anyway i have my bass for now. I already bought a new headunit, just waiting on a new 4 channel amp to arrive then, im sticking in new speakers all round and new wiring! So this is just a temporary fix.
One thing i noticed, my sub sounds louder with the boot actually open. Its not a ported box, and not properly secured to the boot, maybe this is causing the problem