Hello.
 
Please post a picture ;-)
 
Anyways, If I get your drift, I would assume, that it is one of the motherboard standoff holes you are talking about, or is it to do with a mounting hole for the old aircooling block ?
 
If it is a motherboard standoff hole, I would recommend 2 different ways:
1.) to make it two-way - meaning that you allow the waterblock to go flush with the hole, for a small O in the block, so a screw will fit through it, such that both block and motherboard is thightend - this may not look that good though, but would keep both block and board tightend to the standoffs.
 
2.) make a threaded hole in the bottom part of the waterblock, and then put in a threaded pin (like a screw, but without the head), then screw a standoff onto that, and then, (the user : should then drill in that motherboard standoff hole, with a 3mm drill, to allow for the standoff to go directly through, and finally, have a small bolt fit on the backside of the case motherboard standoff area onto it - that way, you will have tightend the block and board to the case, without having a screw-hole in the block (from the top-side - that would be the case with method 1.))
 
At least for my 2 recommended methods, I think that it is best to tighten both block and motherboard to the case - the difference is how it will look on the top part of the block.
 
Best regards: CyberstormXIII