Since you mention RTAS, I assume your PT version is 10 or lower? PT11 and later don't use RTAS plugins. Back to the question; Pro Tools software and all plugins get installed to the C: drive(usually the installers will do this by default). My personal preference would be to NOT partition your drives. Having said that, since both drives are 1TB, I would split the main drive into 500GB for C
system) and the rest as D: for backup only. Leave the other drive as a single 1TB partition(all done as NTFS and BASIC as Pro Tools does not record to DYNAMIC drives). This separate drive would be your recording drive(create and save your sessions here). I assume BOTH of these drives are 7200 rpm? 5400 rpm, 5900 rpm and any "green" drive is a bad choice for a recording machine.
BTW, with 2 drives, any sample libraries should also be installed to the C: drive. The best performance comes from 3 drives(SYSTEM, SAMPLES, RECORDING). A 2-drive system does quite well, but adding partitions does NOT improve performance(and can actually hurt it).