Thanks for answering my question!
Using the stock Slackware 12 kernel (126.96.36.199) I had to turn acpi=off to even get the kernel to boot, so my BIOS was no longer in control of my fans. That's why I needed to do it manually through pwmconfig. But with the latest kernel (188.8.131.52) my acpi works fine so the BIOS is once again in control of my fan speeds and everything is working properly.
I just wasn't sure how the two interacted with each other. Now I understand that my BIOS is in fact controlling my fans, but requires acpi to do so.
Appreciate the information,