Well, for this board I'll be on the safe side and use 2 separate JTAG ports. I'll then try a JTAG chain by wiring those 2 ports together as a learning experience. I'm already designing with both an MCU and an FPGA that I don't have here, and so I can't test anything.
The Atmel Studio did find my J-Link, so hopefully I'll be able to use that. If not, I'll have to order something else. But I did use it before on Atmel MCU's. Sad part is that they're all obsolete and the newest Atmel Studio don't even have them on the list.