markr@cat.co.za said:
>  it seems that once the promise controller is  registered the primary
> drive on the promise controller seems to  become mapped as the boot
> drive

I don't think so:
> atabus3 at pdcsata0 channel 3
> wd0 at atabus3 drive 0: <WDC WD2500JD-00HBC0>
> atabus4 at piixide0 channel 0
> wd1 at atabus4 drive 0: <WDC WD2000JD-00HBB0>
> boot device: wd1
> root on wd1a dumps on wd1b

wd1 is on the onboard controller.

> What is the best way to resolve this ?

Either use /dev/wd1* in /etc/fstab, or wire your primary disk
to wd0 by some lines in your kernel config file like
atabus0 at piixide0 channel 0
wd0 at atabus0

best regards
Matthias