Due to the fact I also have a TF, The hole in the parcel shelf has the removable cover, is there enough room to put one and and then put the parcel shelf on top to hide it? Alternatively is there any factory looking grills that sit flush (much like the speaker covers) A sub in the boot is out of the question. Is the sub worth it or should I just amp the 6x9s instead?

I'd get an Underseat woofer and a pair of splits... Nothing will sound like a sub - except a real sub... 4 Channel Amp under one seat - Nice splits - 4 Ohm Shallow underseat sub.

The sub that was there was about 80 Watts, and I reckon that may have been peak, but maybe not, so 40 - 80 watts RMS at 4 Ohms a woofer in your parcel shelf will what 6x9's cant, strong bass at 40 - 80 Hertz, but dont expect miracles there...
It has to be the right woofer too...6x9's will give you great sound but won't get deep enough if you want a woofer, but either way, deadening the parcel shelf will be best in both cases...
I know nothing about FreeAir woofers, but I can google....;)
But I do reckon that an amped powered woofer in the parcel shelf will rattle so bad you'll never turn it on again....

You can go a fair way towards a large sub using a decent setup with smaller subs in the right configuration. For example, a fellow clio owner has 4 Focal Utopia mini subs (6" i think) in a custom CF box hidden in the rear wings. This is in place of a large sub sitting in the boot

If you are really interested in a free air woofer looking MACH5 audio. They deal mostly in cinema subs etc but their woofers are proper free air with an FS as low as 17HZ!

pm or look at munkymanz ride

been looking at this thread

so i can basically mount a sub on the back parcel shelf?

Yes, there is enough room if you use an 8" sub. My old car was a TE and I fitted an 8 inch sub in the hole with the parcel shelf over the top of it. The shape of the shelf kept it off the sub. The bottom end was significantly better than my amped 6x9s. It definitely won't blow you away like a proper boxed sub. But I actually prefered that about it. The bottom end was really enhanced and remained balanced with the rest of the system (6x9s and front splits).

I did it to keep as much boot space as possible. I sold my boxed 12" for that reason. The better quality 8" had more go anyway!

If only the TJ had that hole!