For the NB, why use push pins? Granted, I wanted to do the same at first as I had very little room to maneuver ( due to large CPU heatsink ) but experienced the same problem with their size. Ended up doing it the hard way but now my heatsink is mounted by screws and I can be sure it'll be in contact with the NB at all times.
I'll agree with DM that you shouldn't need any cooling for the SB. If you're set on it, look for something that mounts like Thermalright HR-05 IFX/SLI. That way the screws / push pins should clear these MB protrusions.
In the end, I guess I'd just go with a small fan near the heatsink. It's the cheapest and easiest to do. I went with a heatsink for the experience of it and I want that board to run for a good few years, so I decided for something more permanent than a makeshift fan.