Sir first of all many of us do not have a dediacted Pre Out for SUB or Pioneer Direct SUB drive.
That Sony AMP (if it is XM 554ZR) is bridgeable and it has a low pass filter to 80HZ.
I have seen 2 SUBs sitting above rear luggage shelf of Alto.
You can just add a JL 12W1V2-4 for 7K Rs in a 11 X 11 X 11 box or a bread and butter Kenwood KFC 3012 or Pioneer 308 for less then 5K Rs.
2nd option, you can have a 12" Kenwood eXcelon XW 1224 or JBL GTO 1214 with a Kenwood M615D/VTREK PS2000 Mono AMP in a 1 CU FT flat sealed enclosure for 15-17K Rs including enclosure.
If you want to go with the 6 X 9 spekaer route, buy 2 pairs of Kenwood S6983 or JVC FX 6922 and a Sony GTR 2002 or JBL AMP as suggested by madhouse12 with some good wooden boxes and 8AWG.
Regards