Should work fine. I have SSDs connected to Sata0,2 and 5 w HDD connected to 4 and DVD to Sata 6.
I'm guessing you want to make the SSD your Boot drive. Either Clone your OS (C: drive), or Re-install your OS and Programs to the SSD (Best Option). When done, just go to bios and set the SSD (Sata X) as your 1st boot priority.
Everything OK then you remove OS from HHD and set it to be Your "D" drive.
If Your HDD is all one large partition and has OS+Programs+Your data and is Larger than your SSD then You will need to correct before selecting Cloning option.