I do a mix of both. I started heavily in traditional painting so to me lighting is super important to be able to just do manually on one layer if I ever needed to. It helps me to understand what it is that the computer is doing digitally.
If it still feels like the blend modes are making really random colors, then I think spending the time to really learn what those modes do would be important. Like using blend modes is weird at first, but it should feel like a second nature thing, where you can predict exactly what a color will do in most blending modes (some of those modes are really heckin weird, but for the most part I can predict them) so even though it's digital, it still feels as comfortable as a traditional toolkit.
If I ever feel like color is getting away from me, it's usaully because I didn't do a color study before I started. Even for pieces that are colored within lines, I like to do a smaller version where I loosely block in color to make sure the contrast is where I want it and that the colors all run together. Especially if there's a strong lighting, it helps a lot to be able to zoom out and really cement down what is going to happen in a quick, rough study. It's an extra step but it saves a lot of time in the long run.
And overall, some lighting is just hard to draw, so I wouldn't be too hard on yourself about it.