Hey there, s25robles.
First I'd recommend that you disconnect the HDD from the motherboard, just to make sure that everything is working properly (that the clone has been successful). If everything is OK and you've backed up any data which you might need from that HDD, then you can just reformat it so that you have a clean secondary storage drive. You don't need to keep any system files or partitions on it if the computer is working fine with just the SSD connected to the mobo.
Hope that helps. Please let me know if you have any questions.
Boogieman_WD