I think you have to go to shematic file, delete just the 1 pin header row, add 3 pin headers, reconnect the microcontroller to the new 3 pin headers and of course power and ground. Then you go to the board, you will have all the other pieces in place, just the new 3 pin headers will be to a side. You drag them to the place you want them to be and retrace from the microcontroller to the headers. Everything else will be in it's place untouched. If you still have remenance traces from the prevoius 1 pin headers, just rip up the old trace and retrace it manually.