>PnP aware OS be disabled /enabled?
Linux is PnP aware, let it sort things out without BIOS interfering, best set it to enabled.
>Power management off / enabled?
For me (Award BIOS '84-'99) it's 'User Define' and almost everything else listed is disabled, except for Primary IDE 0 and 1 as well as Secondary IDE 0 and 1, of course. I'd leave it off entirely in your case.
>Should unused ports ( serial, parallel ) be enabled or disabled?
They're unused as you said, either leave at default or disable.
>Should the peripherals be connected during installation or not?
to see if they're detected or misbehaving. Unless you're troubleshooting really old/obscure hardware, you should leave everything connected.
>Should I put CD in other CD drives, or floppy in floppy drive?
Huh? Just use the CD you're installing from, leave the other drives empty.
Edit: While we're at it, have a look at RTC Resume. It's a function to let the computer start itself every day at 8.00 a.m. for example. You can then set a cron job to run xmms with some music you like. Beats the alarm bell