Unfortunately, repair problems like you are describing are best solved with eyeballs-on-the-job.

Obviously, you realize you've got to stop the water flow in order to properly repair the pipes.

But . . .
  • What are the elevations of the pump / filter / piping relative to the water level in the pool?
  • What sort of valving do you have around the pump / filter?
  • Did you close your multiport, to assure that siphoning wouldn't happen?
  • Did you get a good seal on the plugged lines? (People often don't)

The only quick and easy tip I can offer is that siphoning can occur, but closing your multiport and opening your pump lid will assure it's not happening.

Good luck!