hi vaibhav,
Since you are looking to upgrade here is what I would suggest.
1. Get rid of the bass tube and the sony 4ch amp. I dont know how much you'll get for it but lets assume you would get 4k
2. Get 1 12" sub in a sealed enclosure and get a mono block amp to drive the sub. We're looking at about 18k here. For the sub you can look at cdt, polk mm series, high end pio's etc. These are good SQ subs. Stay away from the loud and noisy SPL stuff like kicker etc.
2. You have'nt mentioned what your running in front so I will assume you are running stock speakers, i.e. speakers that came with the car. Change the fronts to good components. Polk mm6501, genesis, mid level focals, rainbows etc. This would be around 15k.
3. Get your front doors deadened using stuff like dynamat. This makes the front comps clearer and adds a bit of punch to the sound. This would be around 4k
4. Get a good 4ch amp. Again you can look at Polk, kicker, audison and higher end jbl. About 20k.
Total cost about 53K after accounting for your return of sony amp and bass tube. Dont put anything at the back yet. Rear speakers just pull the soundstage backwards, apart from causing cancellation issues and loss of audio clarity. If you must run rears, stay with what you have and just run them off the hu. What head unit are you using? Is it the stock one or an after market unit?
After you have set this up and listened to it for sometime if you still want to add rears you can add the MM691, which in my opinion is the best 6x9 avalable in the market, bar none.
I run a complete polk setup except the hu. Polk makes three series for car audio. The db series is the entry level, the mm/momo series is the mid level and the signature reference (SR) is the top end. I run the mm/momo eries and the sound quality is excellent.