I have seen some videos of people creating ships that launch with smaller ships all in one go. Those ships are often docked with docking ports, which are done from the VAB.
I know that the ports need to face each-other in order to be docked, but when I move and rotate them to face each-other so they are pre-docked, I cannot build things up off of them.
For example, I cannot seem to get a MK1 command pod attached to a clamp-o-tron on top to be rotated to match another clamp-o-tron on the main booster, and then put a fuel tank on top of that.
They won't snap to the top, so the whole thing in super wonky.

am I just supposed to manually rotate and translate all of the parts that are on top?