I've been using a boss GT-3 effects processor and have heard that to get the best you have to check your gain stanges. I find it kills rythmn guitars. Now for recording this is easy, i just can just loose it, but recording live i need to et the best i can from it. I find the sound can go very wooly and loose a lot of qualities but it could just be the way i set up the configuration any suggestions?

Run it in the parallel loop & mix very little of it with your original sound.

I presume this means I should run distortion pedals before the pre amp

Basically, yes. Distortion before the pre, time based effects, after the preamp, where the FX loop nbart suggested resides.

If it gets muddy by running a distortion pedal in front of your amp then there must be something wrong with settings you use. The most common mistake is too much gain.

Other than that Bazz nailed it.

I seem to have issues with my parallel effects loop, its an orange, and I have this odd feeling you cannot get rid of the dry signal in the GT-3 therefore you are left with 2xdry ignals and of course due to the small delay you get some interesting phasing. I'll keep playing and see what i come up with.

You should be able to control the level of wet & dry. Turn it to 100% wet.