Smart Scan with Rescue Disk, and two system drives

I have got two system drives (two SSDs), which both contain Windows 8 Pro 64bit. The operating systems have been installed completely separately, which means that when I was installing one, I physically disconnected the other SSD. Now they are independent, and I choose which one to boot from BIOS.

I am using Comodo Rescue Disk, and am interested about the Smart Scan function.
How do I know which one of the two system SSDs will be scanned? Is there a way to choose which one to scan with Smart Scan?

Similarly about the Custom Scan “critical areas and boot sector” option: which drive will be scanned with this option turned on?