I have gone through the same dilemma and would like to be as much helpful as I could. I have to same car with stock navigation and I discussed the matter with a lot of guys including @sheryar bhai & @madhouse12 and some good sound system installers personally.
The problem is that stock headunit is not just a head unit but a HVAC system (Heating Ventilation Air conditioning) as well, you disconnect this unit and will lose a lot of vital features and the front look of the car. Now there are two places where secondary head unit can be installed:
1. Under the stock navigation
Possibilities:
1. Either buy a DVD fascia and install new 1din unit along with the nav disk panel (actually the ROM). You'll lose that pocket under the ROM which I use to keep my wallet while driving
2. Rewire the nav disk panel @sheryar bhai did a diy and relocated the ROM under the driver seat, I didn't opt for it after a lot of thinking) and install the headunit with a 1din fascia (or the same panel but that cover will look real awkward) and you'll save the pocket underneath
2. Under the Driver/Passenger seat
A simple installation and the unit will be held securely with a few clamps, remote sensor will be relocated to the front but you'll lose the functionality & usability. On the go fine tuning etc until you learn by heart how to activate deactivate change eq settings by heart or every now & then you'll be parking your car, opening the door, facing down the seat and adjusting the ***** settings - It's No Fun!!
3. There is no other Good Place except Trunk
Yes IMHO the second best place to locate your headunit is trunk, you must have seen that 6 CD changers in trunk? yeah like those a tray hooked with the trunk top & you'll be at peace. Also this would be much better & practice then the under seat idea every dumb installer will just (Sir jee sensor upr le ayein ge)
Drawbacks:
1. You'll loose bluetooth connectivity - speaker disconnected - no purpose of pairing your smartphone now can't hear the other side when on call.
2. If you car is voice activated you might enjoy when she talks with you?
"eeenchoj me kong falaan teeng seatbelt" - wear your seat belt
"Altu Jalaltu Aii Bala ko taltu" - When you are cruising peaceful and cross the speed limit set in your car, mine is 110
& other scenarios which we the owners know
YOU WILL LOSE THIS FEATURE AS WELL when the driver side door will be disconnected.
More Importantly
When I was at your stage & came to know the drawbacks mentioned above I took a wrong decision & installed an expensive sound system without changing the original headunit
The result was as expected
1. The sound started clipping even at 0 gain on some songs (with high treble beats)
2. There is a permanent hissy sound in my speakers which is very much audible until sound level 4-5 when you're driving in a peaceful environment killing the purpose of drive -_- I have tracked everything its coming from the damn headunit. THD it is because it is present in your stock speakers as well if you'll hear closely.
Currently I am living with until I'm done with my FYP but its a real PITA rightnow.
Solution
The only solution that will fix all these things will be a DSP attached with the original headunit and then rerouted through any system(amp/speakers) you like and this was suggested by @madhouse12 but this DSP thing is gonna cross your budget limit.
Now whatever route you'll go with but its a lovely car so please don't screw it looks or at least I'll never forgive you :@
P.S. forgive any grammatical crimes I might have commited as I am too sleepy right now to read all this crap once again from top