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I wanted to position the subs firing toward the cabin of the car. Now I want know if it will sound better if I fire the subs toward the trunk lid or will it sound ok firing toward the cab of the car. The reason I want to have the subs firing toward the cab is just for aesthetics.

I was also contemplating cutting a hole in the rear deck and having the subs firing up, directly into the cab of the car.

Which will sound best and what kind of problems will I have?

The car is a 96 mercedes c220 and the rear seat does not fold down.
The subs are two MB Quart PWE 302, which are dual 2 ohm subs.
The amp is an MB Quart raa1000 which is stable down to one ohm providing 1000 watts.

Here are a couple of idea that I have:
subs firing up
Same as my trunk

by aesthetics, do you mean you want the subs unseen, since the seat is fixed in location?
if so, consider venting the rear package shelf to couple the air of the trunk and cabin, then firing the subs toward the rear of the car, and building a baffle board to cover the face of the box, and covering that board in acoustically transparent material like speaker grille cloth or headliner material.
That'll hide the speakers while giving good results acoustically.

I have mine firing towards teh back of the car and its great... i don't have enough speaker cable left to point it foreward or i'd try...

By aesthetics, I mean for show purposes. The reason I wanted the subs to point towards the back seat is so I can put plexiglass in the rear of the box so I could see the magnets of the subs. I am always use to putting the subs facing the trunk lid, but I wanted to see the magnets of the subs. I was confused if the subs will sound good facing the back seat.

I was thinking if the subs would not sound good facing the back seat, I would cut a hole in the rear deck, because I think that it would sound good like that and still give me the option of seeing the magnets of the subs.

if it doesnt sound good you could always invert one or both subs to show off the magnet while still point them towards the rear of the car.

Thanks for the replies, I was looking at the faq section and found a lot of answers. I was confused about building a baffle to seal the trunk, how would I go about doing something like that?

If you desire the best performance and have the time and/or money, then the example in fig. 4 is the way to go. First, a baffle must be built to seal the trunk completely. The baffle should have a hole that the speakers will fire through. The angle of the sub enclosure's front face should match that of the baffle. Slide the box up to the baffle and screw in place. When done correctly, bass will not be able to enter the trunk and cancel. Once complete, try this test : Sit in teh car while the system is playing (with doors and windows closed). Have someone open and close the trunk, there should be no difference. If opening and closing the trunk still makes a noticeable difference, then the baffle must be sealed better.

You can see figure four HERE

in a nutshell either against the back seat or the rear deck you need to construct a baffle, basically another piece of mdf will work, and seal the edges so no air gets around it, you will have to cut a hole in the center to allow your subs to play through. then mount the sub box to the baffle.

How would you mount the baffle to the rear deck while making sure it is completely sealed and then how would you mount sub box to the baffle?

well, the baffle just consists of a thin frame that fits over the face of the enclosure, covered like a speaker grill. If you use plywood, you can use a solid sheet, and cut openings where the speakers sit, exposing them to air, but hiding them with the cloth covering.
the baffle is removable if you want access to the speakers, but otherwise it keeps the entire system totally stealth

were you aware that using lexan in the way you intend, is going to require 3/4" to 1" lexan? That stuf requires a lot of work to finish the edges, and seal that panel so it's both sealed and looks good. It's also about $800-1200/sheet for that thickness.
just FYI.

venting the rear package shelf will actually benefit you regardless of speaker direction though since a MB has a very well sealed trunk, and couling the air from the trunk to the cabin always helps.
so does stripping away the insulating materials between the rear seats and the trunk.

That is expensive for plexiglass, I was hoping it would cost a little under $150. I thought I would just use 3/4, but I wasn't sure exactly how much I was going to use and how I could do it. Is there a way where I can still see the magnets and not have to spend so much?