thanks for the replies. in total it has been running for about 2 hours. There are lots of bubbles stil in, from reading a review an what I've seen my self is that the pump just churns the water up in the res and the bubbles keep getting re-circulated. I've tried filling it too the brim. Maybe I'm just being too impatient, its just that there was no apparent reduction in bubbles after 2 hours. I don't know if the problem is that the inlet is near the top of the res with only a few mil of water above it. In another thread I posted about bleeding problems it was suggested that I try bleeding without the pump running but the outlet hole isn't at the top so you have to tip it left and right to get air out and I was getting no-where with it and lifes too short for that.
This is my first time at watercooling so I haven't got a t-piece or anymore tube left, I think I might try a T though, it could be a cheap solution