You'll have to drain the loop either way. Whichever is easiest for you. Normally the best place to do it is at the lowest centre point of the case so gravity can push most of the fluid out. If you can drain it over a basin without getting fluid on your hardware, then do that, then just add in the waterblock. maybe best to cover up your PC components and power it down of course to be safe. Also bare in mind that adding a card to your loop will increase the fluid temperature, so make sure your rad has decent fans and is at least a triple rad. Anything less and the cooling would likely be inadequate.
Cheers, just wasn't sure the best way to do it, but I think I will remove it, also I will be running second rig in a few days, what will be an appropriate rad size for 1 7950 and an AMD sempron 145? would a 120mm do fine?