The FastATA bypasses the onboard IDE so I don't think you can connect directly to the Motherboard IDE, I'd imagine it would not work and potentially cause other issues.
I have the same setup as you (except I have 060/PPC) so I have FastATA MkII/Voodoo/Mediator SX
I also could not run a 2.5in HDD off the 44way connector on the FastATA, instead I use CF cards off this connector or you can use 3.5in HDD off the 40way IDE.
Here is a cool tip for you, if you connect a CF-IDE adapter to the 44Way IDE on the FastATA and a 3.5in HDD to the 40way IDE CF will take priority if you have a CF card inserted (it disables the 40Way IDE) and if you leave the CF unplugged then the Amiga will boot from the 40way IDE with the CF disabled. Cool eh?
I use this for my multiboot setup, i.e I have OS4.1 Classic on a 3.5in HDD on the 40way primary and a couple of CF's with CWB P96, etc.
I have OS3.9 on my BPPC SCSI (Via SCSI-IDE) and if I insert a blank non bootable CF in the CF-IDE it disables the 40WayIDE in the and boots from the SCSI. You can still use the FastATA driver to use a DVDRW off the secondary IDE and the 44way IDE (with blank CF) is available for file trasfers.
Hope that helps,
Steve.
