If you HDD has a boot partition (and you won't be installing linux) use it... if you use PS2Menu this partition will always show up...
as for the 48-bit... if you don't have a drive over the 127GB limit don't worry... if so make the partition at the beginning of the drive... as llong as you haven't passed the 127GB limit you should be safe at making a partition... you should make one larger than what you will need... incase you want to add stuff later...
PS3 Slim 320GB
PS2 v11 exploit w/300GB Maxtor
PS2 v10 exploit w/80GB Samsung - Network Games
PS2 v10 exploit w/60GB Samsung - Network Games
PSP 1001 3.52M33 w/10GB total storage
NDS DSReal 4GB