As I recall, when I first used it on my AMD board with a FX-8150 chip:
1) I removed the fan bracket that was installed on my MSI MOBO.
2) I put the 2 adhesive strips on the rectangular plastic back plate that came with H20
3) Installed the metal nuts into the back plate
4) Installed the back plate to the back side of the MOBO
5) when you assemble the pump fastener ring, make sure the plastic bits are installed correctly, I believe this is where you will run into the alignment problems. because there is 2 plastic pieces that snap together for each screw and they are offset. You have to refer to the manual to determine which way they should be installed. If I recall, the offset should be towards the outside for all 4 corners pushing the screws outward.
6) after assembling the screw clips and you install the screws, then put the metal ring over the pump and from the other side, snap the plastic ring into the metal ring, THIS REQUIRES A BIT OF EFFORT TO DO
7) Then at that point, you should be ready to set the pump on top of the CPU and screw the screws into the back plate I STARTED THE OPPOSITE HOLES FIRST, IT TOOK A BIT OF EFFORT BUT IT WORKED FINE.
Look at this picture from the ANTEC manual. you need to make sure that the clips are installed in such a way that the screws are furthest away from the pump
Clear as mud???
Hope this helps.