I'm putting in new 6 by 9 speakers in the rear shelf of my ba, iv come down to 2 choices Rockford fosgate or jl audio they will be run through a 4ch amp, which brand do u guys recommend ?

I only use Rockford fosgate, best gear especially if you go the power series. I haven't had Jl audio before so not sure about them. I've got Rockford all round in my ute and currently installing full Rockford power system into my old mans Bf GT apart from a punch amp for front speakers.
If you have decent speakers in the front then before you connect your rears into the amp run the system with just fronts, and see if you like the sound. Just the two front speakers and a sub clears up the sound so much I reckon, so only 6.5'' splits going into the GT at this stage with the removal of rears for more bass to ener cab. Much clearer sound!
And are you surface mounting them or cutting the shelf? I thought ford only used 5x7's in the B series? That's what are in my ute and the GT aswell

Go Hertz HCX 690, will sound better than both.

I always recommend amping the fronts prior to amplifying the rear speakers. Doing the rears instead draws the sound to the back of the car and sounds horrible.

Amplify the fronts, and if you've got a sub I suggest using a 6 or 6.5 inch coaxil or split set in there instead of a 6x9. 6x9's tend to distort quite easily being that the cone is actually an oval shape, so if you have a good look at the cone and surround with a microscope you will see that the whole lot actually hits in an uneven fashion where as a round cone speaker is actually more control and has the potential to sound a hell of a lot better.

Now if you don't have a sub 6x9's are a good option for someone wanting just that extra little bit of kick, but once again if you are not planning to amp the fronts then I dont think your going to be too happy, so once again I advise amping all the speakers if you dont have a sub otherwise just amp the fronts.

Now as for brand, brand most of the time doesnt mean a hell of a lot especially with entry level gear, DD (Digital Designs) make some 6x9's that are designed the take a pounding, Rockford with the larger than normal surrounds take a bit more of a trashing where as you will probably find for sound quality the JL's would be better. However the best idea is for you to have a listen for yourself prior to making a choice.