1. ONLY create the System partision (the one holding workbench), it should be within the first 2GB of the drive, it can be 200MB or 2GB, doesn't matter. Bootpriority 0 is fine and dandy.
2. Install the OS on the System partision. (Personaly I do it the slow way of installing 3.1 first and then CD drivers for OS3.1 and finaly 3.9 but if you have a bootable floppy with CD drivers I think you can do it that way instead).
3. Install Boingbags 1 & 2 (these help with bigger drives)
4. Now that the OS understand the bigger drives you can start creating the other partisions as you wish... as big or as small as you see fit. None of these should be bootable and thus not have any bootpriority. Partision names are individual, personaly I like to have at least 3 apart from System, being Work, Games and Saved. On bigger drives you could go all crasy with partisions for Demos, Graphics, Music, Temps, Miscs, Programming, Security etc... all up to you and how much memory you have (every partision uses up a bit of memory).