From my understanding it looks like you would like to use System Restore to restore to an earlier date of your operating system installation. Actually, it is unlikely that your operating system spans across multiple drives so what you're trying to achieve will only be done on the current operating system you have booted in to (drive C:\).
If you have multiple installations of the same system image on the two drives respectively, then you are okay to go ahead and boot in to them individually to utilize system restore independently on each of the drives.
If they are the same images then you are likely to have the same restore points on them.
Can you please elaborate on what you are trying to achieve?
My Computer
At a glance
Windows 8 Pro x64i7 3820 @ 4.68GHzF3-12800CL9D-8GBXL (32GB)GTX 480 SLI
Computer type
PC/Desktop
OS
Windows 8 Pro x64
CPU
i7 3820 @ 4.68GHz
Motherboard
ASUS Rampage IV Extreme RoG BF3
Memory
F3-12800CL9D-8GBXL (32GB)
Graphics Card(s)
GTX 480 SLI
Sound Card
Auzentech X-Fi HomeTheater HD
Monitor(s) Displays
Sony 32V5500
Screen Resolution
1920 x 1080
Hard Drives
LSI MR9260-4i (RAID10):
Toshiba DT01ACA300 x 4
iaStorA:
OCZ Vertex Enterprise 120GB
ST3500320AS 500GB
Intel 520 Series 120GB
PSU
OCZ ZX 1250W
Case
HAF X
Cooling
H80
Keyboard
Cyborg V.7
Mouse
Razer Lachesis 3.5G 5600dpi
Internet Speed
23296kbps ds / 812kbps us ADSL2+
Browser
Mozilla/5.0 (Windows NT 6.3; Win64; x64; rv:32.0) Gecko/2010