That is a matter of personal preference, e.g. what OS versions you like to run and the available disk space.
I run e.g. Windows 7 in Virtualbox with PCLinuxOS as host, so I have no issues with a dual boot. I also have no interest in using any other Linux distribution than PCLinuxOS. That make things quite simple.
I too have two disks (on laptop as well as on desktop); and they appear as sda and sdb. Both are 2TB on my desktop and they are of the same type and brand.
On sda I have 1 primary partition (sda1) and 13 extended partitions (sda5 until sda17). Of those 13, 1 is a swap, 7 are ext4 and 6 are NTFS
On sdb I have also 1 primary partition (sdb1) and 12 extended partitions (sdb5 until sda16). Of those 12, 1 is a swap, 6 are ext4 and 6 are NTFS.
The sda1 partition is a small dedicated boot partition. I have set that up recently, because I wanted to have a main system and an identical bootable backup copy. For Win7 I have the VDI files (one per VDI virtual hard disk) stored on one NTFS partition and the same applies to two (with Virtualbox) shared data folders; each has its own partition. The partitions on the other disks are backup partitions and spare partitions for new versions of PCLinuxOS. I'm e.g. planning to install the 64bit test version one of these days.
Currently my / is on disk 2 and /home is on disk 1 and the swap used is on disk 2.
I find having the dedicated boot partition particularly useful.
It is a personal setup. You may prefer an entirely different one.