Linux from scratch question

Hello:

I know there are many hardware compatibility issues to pre-check, but in
general, when installing Linux from scratch on a new hard drive, out of the
box, should I boot from the Linux floppy and let the Linux installer do
everything to the hard drive (Linux equivalent of fdisk) and not use the
floppy that came from the HD mfr.? It's a 20.5 GB IDE drive (oh man I just
thought of another possible hardware compatibility problem...the drive came
with an ATA 66 accelerator card...which is probably a PnP card...is that a
problem?

Thanks

Murray