Are you saying, y'all are upgrading your panel, and when it's upgraded, y'all are going to add four more circuits? Are y'all re-wiring your box?
As you said, if you choose to drill through lumber, drill through the center mass, that area is neutral. A safe rule of thumb is don't remove more than about 1/4 of the woods width, but, you can look up the specifics based on your dimensions and situation (load bearing/not load bearing/etc.)
But, there should be fairly minimal need for drilling new holes.
So, are you going to need to create access for everything, or is it all open?
What is this going to be used for, what kind of loads are you going to be putting on each run.
Care to take some pictures?
If you want some help feel free to hit me up, I've been pretty busy lately, but I'll try and get back to you within a day.