Thanks addy - that flagstone in the pic above is actually for the water to fall over, not the weir cover (in case you were thinking that) , i was going to put the weir behind that again , maybe a step above so the water flows out of weir, onto a stone , onto the smooth stone and then into the water.
I am just worried I will be losing water out of the weir if its not sealed correctly around the liner so i suppose I could sit it on the liner and let gravity take course or use my other suggestion and clamp liner to it .
Another option is to make a weir from liner and stones but the problem there is how to secure the 2" pipe into this .