you can go a few ways as far as partitioning your drive: you could create separate partitions for /,/home,/usr,/tmp,/var (& swap), or you could use one big root partition & a swap.
having /home on a separate drive means you won't lose all your files if you have to reformat/reinstall linux, so a lot of people just use a 1 - 2 gig for root, and the rest for /home (mine's 4 gigs).
the general rule for swap is swap size = physical ram - up to a point, though. anything over 256 MB swap is overkill - especially on a workstation.
using the 2nd ide channel won't be a problem.