Im hopefully fitting my amps and sub this weekend.

Only problem is, is that my parrot kit runs through the normal speakers. these will be run through my amp, not the head unit.

is there anyway i can get the parrot to work still?

Yes.

Use the two flying leads for audio out and either terminate them in the head unit with the green connector such that they operate the head unit's phone output.

I'm guessing currently you are using the phones piggy back ISO connectors, so just disconnect the speaker side of it in exchange for this. (It's all in the manual)

You will also need to wire up the phone mute if you haven't already.

Yep,

I did exactly as described above over the weekend - used the green block to plug into the back of the headunit. It works fine. Not sure what Parrot kit you have but on the 3100 they used to be the loose green and brown wires in the cabling that you could connect to the radio line in (I crimped my own cables). If you have an aftermarket headunit and want to plug in using standard line it (phono style plugs) then you should be able to crimp something together. I know Maplin do the Yellow external amlifier block connector blocks with Phono/RCA plugs already on them that you could modify. Might make the connections a bit easier if you need to start with the plugs already on the cables. What headunit are you connecting to? Will it accept the Green block type connector like the VAG units or does it have to be phono/RCA type plugs?