Plug in anything Sata, which will be the ssd/hdd. Once that's done, there's honestly no reason to remove them, so a gpu covering the Sata ports is a moot point. At worst case scenario you use 90°sata connectors if the mobo has top load headers, or plain straight connectors if the mobo has sideways Sata headers. Either way, it's only a pita concern if you plan on changing Sata with any frequency, which never happens with most ppl.