My process was angle grinder for cleaning/scarring surface. Wiped with acetone to further clean. Applied a 2 part epoxy around the hole, then caped it with little 1"x 1" metal cutout. On the smaller holes I just used epoxy.
Plan on covering/Insulating the floor down the road. So the little metal cutouts wont even be noticed.
FYI I am a complete skoolie noob as youself. So take as much or as little weight in my technique as you want.