I don't have this board but judging by the product page it has a USB blaster interface that you just connect a mini/micro cable up to it. This should be independent of PCIe so I think it should be safe to connect. You will have to install the driver for the USB blaster assuming your workstation does not already have it installed, I'm guessing the kit came with instruction on how to do that. For development work I always leave my JTAG connected to my OpenCL board so that I don't need to open my machine any time I need to flash program the board.