Normally, I would not notch joists at the bottom. This is the worst place to cut into a joist from a strength standpoint.
But If You Have to:
For every location where you are going to notch, I would first take an 18 inch length of 2x4, glue and screw it firmly right along the bottom edge of the joists. Center it where the notch is going to be. Then cut your notch through the joist and 2x4 just deep enough to fit your pipe into.
Be sure to install a metal plate over the pipe at the notch so in the future you or someone else doesn't puncture a hole in the pipe while trying to hang something from the ceiling, or while your installing the drywall.