First off, knocking can mean alot of things, ultimatly its total engine failure so be carefull before you go revving the t*ts off it. Now the VR6 engine layout means it does sometimes suffer from a bit of piston slap which is a knocking noise from the pistons when its cold, very bad cases it will only quieten slightly when warm, go for a drive, if it knocks harder on acceleration and goes quiet on deceleration.. thats piston slap, not something you need to worry about too much! If the knocking gets worse when you rev the engine and carrys on during deceleration, it could be the bottom end, but unlikely! Any noise from the top end should be a lighter ticking/tapping noise. The timing chains can make a tapping/light knocking noise.
First off, get the air out of the pipes, they can be a pain, start the engine up and run it, take the top off the coolent bottle (while cold) and massage the top and bottom pipes with your hands, pumping them. do this at idle, then rev it to about 2500 rpm for about 60 seconds and pump the pipes again, you should see a bit of air bubble out of it, by the sounds if it you dont have much air in there, then run it up to full temp (Keep the interior blower on full HOT at all times) just incase it does overheat. put the top back on the bottle, sit in the car and watch it warm up to full temp, Watch that gauge though!! wait for the fan to kick in and check it cools it off and doesnt run above half way.
