Should work OK in the 2nd slot. You will need to set the boot priority in the BIOS to make sure it is booting off of the SSD. If for any reason you have problems in the 2nd slot you could always just swap the drives. Before you wipe the spinner I would remove it from the system and make sure you can still boot properly from the SSD. You don't want to burn your bridge until you're sure you don't need it.
I'm not familiar with the Samsung software but if it says it's designed to clone Windows 7 then it should work. The only question might be whether it will clone the restore partition and whether that is even something you want. Many people don't want the restore partition anyway because it takes up precious space on an SSD.
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