It's fine to divide your harddisk into more partitions. But you won't gain much, if any speed performance out of it. But for systematic reasons, more partitions is fine. I would make the sample partition bigger than the OS partition, as samples libs does fill up a whole lot of space, especially if you have or plan to get more samples expansions. But if you have lots of programs installed on your OS, then 200GB might be just fine.
Many people buy a second harddisk, and puts it on it's own motherboard disk controller, and then use it for samples libraries, projects and such. And then use your first harddisk for the operating system. This will give you a little speed performance, and you then use two separate HD controllers. One for the OS, and the other for samples.
I don't know about the x48 you mention, what it is. But if you upgraded a studio4 to studio6, then you should be able to start them directly with their own icon on your PC desktop. I think you should have two icons, one for v4 and another for v6, as both versions have their own profile & folders. That's how it works with the full Cubase versions, that I use.
You need to setup a path to your plugins in Cubase studio 6. That's why you can't see them. Go into the plugin-information setup window, and click on the VST path tab. Check, if you have a path to where you save your VST 2.x plugins. If it's missing, just enter it and save. Then, the next time you load Cubase, the VST 2.x plugins should be there
All the best,