Unless you basically made the SSD appear as part of the mechanical drive, Intel MB's can do this, called SMART RESPONSE TECHNOLOGY, you have to use the SSD and the Mechanicals as independent drives/partitions.
Generally speaking, most people will use the SSD for the OS and maybe a couple of 'always used' programs. This affords fast boots and shutdown and faster loading of the needed applications. Still, even starting anything from the mechanical drives still requires OS files access, so it isn't just not accessing the SSD. For an SSD, one generally wants to move most non-system data off of it, but some data for applications are probably best left on C: anyway (stuff that goes into C:\USER and the Registry for instance.
I've got a 115GB Corsair SSD, and it really is smaller as that spec's includes the 'extra' sectors. It actually is 107GB's in size and I have 50GB's free, and this is after over a year of use. Carefully management of what goes onto C: makes it easily manageable. I *DO* have MS Office installed on C:, as well as Norton Ghost, and an e-mail Client, as well as Firefox, a few needed utilities, and Quicken. All this because if I should need to re-install the OS from back-up I want these programs complete and at the same level.