For me personally, I have my partitioning scheme as follows on my laptop which houses a 320GiB hard drive.
Swap = 256MB (I have 4GB of RAM installed in my system)
/Boot = 256MB - formatted to ext2
Everything else is formatted to ext3
/ (root) = 20GB which should give me more than enough space for my OS to grow
/home = 25GB
/home/Pictures = 25GB
/home/Documents = 25GB
/home/Downloads = 25GB
/home/Music = 150GB ( I have a lot of music!)
/home/Videos = 25GB
Then whatever I have left over, I can put to use at a later time.
Most partitioning schemes are generally personal preference, as long as you set your partitions in the correct order (i.e. having the most accessed partitions at the beginning of the drive). There's a very informative thread HERE
written by Fred if you need any other tips to help you in your decisions to partitioning.
Since you have 2 drives in your system, it's basically all up to you as to how you really
want to set it up. Good luck!