You can try to do pad-over-pad but this will probably generate a Design Rule Check (DRC) error.
You should be aware of Altium's "electrical grid", if not look up in the knowledge center. I believe the shortcut is shift+e. The electrical grid causes the cursor to "snap" to electrical connections.
What I would do is delete all but one pad for each footprint. Then I would grab the part by the pad that matches the one not deleted; Altium should "snap" to grabbing the part by the center of the pad the cursor is over. Drag the component overtop of the undeleted pad and the component should "snap" into place. Let go, and you'll probably be meeted with the ugly green DRC error highlighting. Click the undeleted pad, Altium will list several things under the cursor, select the pad, and delete it.
Another way to move the component if you happen to know precisely how much distance you need to move can be found under Edit -> Move -> Move Selection by X,Y... In fact, I have set up a shortcut for this action.
BTW, you said you were new, so forgive me for asking...but do you have a schematic for your design? I've never personally went "this direction", importing step files to get component positions, it was always the other way around with me exporting my PCBs for the SolidWorks guy, and then if he needs me to move a connector I Move Selection by X,Y... to match whatever he asks for.
Try this:
Go to the PCB.
Click Project --> Component Links.
Make sure all the parts are linked.
Click OK.
Go to the SCH.
Design --> Update PCB.
There should be nothing to update.
Best Answer
Turns out it was sort of an artifact from earlier PCB 'experiments' on the same board when it wasn't done, went to Design -> Netlist -> Clear all Nets which solved the problem.