Your second disk doesnt need the bootable flag. Only the partition to boot from on a disk will have that flag. If its gonna be a primary or logical partition is up to you. A disk can have 4 primary ones max, if an extended partition is needed to hold logical partitions it counts as a primary one.
If you're adding the partitions at install time, having em marked for (/bin, /sbin, /boot, /lib, /root, /usr, /etc, /var etc etc) will add files under that, and you don't want that. Adding this disk can be easily done after installing your OS as well.
Install OS. Partition 2nd HD.
Run "mke2fs /dev/nameOfPartitionOn2ndHD"
Add line to /etc/fstab:
/dev/nameOfPartitionOn2ndHD(tab)ext2(tab)/files(tab)defaults 0 0