@Mightymilk
Partitions are a great way to get the most out of your hard drives in my opinion, not to mention the fact that if you have your OS on a seperate partition from all your data then reinstalling an OS isn't near as big a deal since you don't have to back up all your data beforehand.. though it is still always a good idea to create backups periodically
.. But having multiple partitions is an extremely efficient way to use a hard drive IMO.. The only annoyance is that you will have to reinstall all your apps, but you have to do that with or without multiple partitions anyway so that's nothing new...
And as UBF said you shouldn't have any problems doing what your thinking with your drives.. I think in the end you'll like having partitions rather than everything on one drive too..
Good luck!