I would manually copy the photos to your computer, figure out which ones you actually want to keep, and them copy them back to your SD card, either via USB 3.0 reader (which would be a lot faster for that much data) or via USB cable through the phone itself. I haven't used SmartSwitch to copy files to/from SD cards, since I can just drag and drop the entire "DCIM" folder and copy it to my PC's hard drive to back it up.
(I just tried to manually select a folder from a backup of an internal memory category (music) and restore it to my S7 via SmartSwitch. Even though I have an SD card installed, I was not given the option to select the destination of the "restore" option, so I suspect that you will not be able to use SmartSwitch to move your photos from your old S6 internal memory to your new S7 SD card. I would stick with copying the DCIM folder manually. It's a piece of cake.)