Is is normal for a 16 bit to take a long time to save?
Not in my experience. A 16-bit file will be about twice as big as an 8-bit file, but on my system I don't notice any significant difference in time to save. They're both fast. How big are the saved files?
And in After Effects I had my scratch disc set to the SSD which is too small so I just changed it to the D drive. It is set at 50 and wonder if allocating more space will help AE since I run out of memory?
Also, what is the Conformed Media Cache? Should I change those folders too?...the Database & Cache Folders. Should I clean the Database & Cache? I periodically empty the disc cache.
I would not put either of those on the SSD system drive. The default location is in your user data (which is on the system disk), but that's not ideal. Adobe recommends putting the Disk Cache on a disk that is not the system drive or the drive where the source files reside. If you can't, don't worry about it. The disk cache is used heavily in AE CS6, that's where the global performance cache resides. The size will increase with use up to the maximum you set. 50GB is reasonable. Professionals working on many (or large) projects may want to increase it. I empty the disc cache whenever I finish a project.
The media cache database keeps track of the media cache files. These are the .cfa, .pek, etc. files. The media cache database is shared with Adobe Media Encoder, Premiere Pro, and Encore, so each of these applications can each read from and write to the same set of cached media files. Each application can use its own cache folder, the media cache database keeps track of them all. The Media Cache location is where AE will store the media cache files if they don't already exist. The space will continue to grow, so this is not a great candidate for an SSD. The clean database and cache button will only remove entries and cached files if the source that they correspond to is gone.