I'd suggest you work in and around the islands where you can shelter from the winds, should they be up
where to go depends on what species you're targetting
For size Red Emporer you generally need to be in around 30-40m of water, out near/past where the iron ore ships anchor in the area that used to known as "the killing fields"
once you find this area - it's very non descript - not much structure around but when you find some there will be fish around.

flying foam passage holds some coral trout and bluebone; corl trout are territorial, but the bluebone will cruise around

there are still a lot of fish up there but many years of LNG and Iron Ore Projects' temp construction workers have done a good job of cleaning out the easily accessible reef systems
I'd suggest joining a club, like Nickol Bay Sportfishing (that's what I did). 
They won't give you marks but they are a wealth of knowledge, and will point you in the general direction once you earn your stripes.

also look at the barra fishing scene up there; better than I expected

most of my best fishing memories are from my days in Karratha/Dampier;simply aweseom fishing

 not sure why your not finding bottom fish around the pipeline..  Are you heading outside the shelter of the islands?  Usually where the pipeline splits apart you'll find Rankins and a bit further out will be reds (and sails, marlin).  Plenty of fish where the water drops off just on the outside of the outer islands