...you didn't mention any other specs about your machine...CPU, GPU, system memory, etc.
Generally, only operating system , programs , and Windows page file should go on your "boot drive" SSD. You MAY however place the "media cache" and "cache" files from Premiere Pro there as well. Bill Gehrke has done testing and found NO performance penalty for doing that. It also makes it easier to erase those files upon completing a project.
ALL OTHER FILES related to PPro should go on the PCI SSD, as this is your FASTEST DRIVE and this drive will provide the best performance. That means : media files, previews, media cache, cache, and exports. There is NO NEED for a separate drive for a "cache" . You could experiment where the "global performance cache" for After Effects is placed, to see if it makes any difference...I would guess the best performance would be on the PCI SSD. The PCI SSD should be providing around THREE TIMES the speed of a single SSD.
As the PCI SSD is only 400GB it looks like you must use it as a "work drive" to provide the best speed and performance, and THEN you must move completed project files and media source clips off to another drive to archive and backup.
As quality SSDs are getting much larger and have more reliability at a cheaper cost.....they will serve well as archive and back up drives.
Spec wise i'm running
Windows 10 PC
Intel 5960X Extreme 3.00GHz (overclocked to 4.3GHz)
64GB DDR4 RAM
GTX 980 G1 Gaming card (o/c to 1355 / 1455 boost
your right about the size of the PCI SSD - i purchased a Year ago but think they have come down in price