I do crap like this too, but just know, those "premarked indentures" were in fact, the spot welds holding the things together. You just drilled out two structural body/door welds. In the future, i recommend using a center punch and making a new hole - ideally big enough to fit a grommet, then goo everything up with black rtv at the interface when it is done to weatherseal and reduce movement. I'm sure it will be fine, but if you truck is anything like mine, it can use every bit of good metal and good connection that it has left lol
Yellow isn’t power that’s the constant the red one is the 12 volt run the yellow wire to a constant power source and you can run the red one straight to the battery