Heres how my hw is set up. First of all, power is pumped into both the original connector and the floppy port connector. Some tower setups only connect the -12VDC line through the original connector.
1) There are a couple of chips next to the PPC that can get way hot. I use a mica (non conducting ceramic) disc and heat transfer compound to ensure that theyre in good thermal contact with the heatsink.
2) An AMD K6-2 heatsink sits on the 040, but no fan due to space limitations...
3) A power amplifer heatsink (copper, 1 inch tall vanes) is attached to the Permedia with heat transfer compound.
4) A 3.5 inch case cooling fan is mounted just above the BVision/BlizzPPC assembly to ensure good airflow through the system.
Everything runs just fine...