Okay, thanks everyone.
I just wanted to double-check what I assumed to be true because I had
to fix a Molex connector (some of the wires had gotten a little fray),
and it did not occur to me to pay attention to which holes the the two
black wires were connected to (I guess that subconciously I knew them
to be the same for obvious reasons and so hadn't bothered).
After I put the yellow and red back in their places, it occurred to me
and I was a little worried that perhaps the grounds were meant to be
specific to the different loads or terminated at different places (for
example one goes to a resistor or something before heading to ground,
etc.)
I've been told that in many cases they actually connect back in the
power supply which is what I figured, but could not be sure of since
there are two distinct wires. My research (which found this subject
to be rather sparse since the focus is mostly on the positive leads
and pinouts), found that the reason there are two is due to older
drives and PSUs in the past which often used wires that could not
handle the combined load and so had separate ground wires. I've been
told that the wires used today can usually handle it just fine (so
one could do but the standard is already set.)