You are not going to get any true bass from 6x9s, you get midbass at most, no matter how many you put, those speakers will not perform well on boxes, are designed to work in infinite baffle settings like your rear deck, will loose low end. 3 way will pickup earlier midrange frequencies which the big oval driver can't reproduce accurately.
There are very good and inexpensive subs to choose from that will get you real bass (30-40Hz). Take a look:
MB-Quart-FWA-304D