I just got done exploring this for myself. Basically, there's a texture folder for each design type. I would copy it and immediately create a backup for the ride you want. The trick I've discovered is, each file follow's a few different mapping templates. You'll see one in color, and one in grey scale. These are the two you want to change. If you edit the color one, that is the "top layer" color which will show. The grey scale helps the coaster know what layers you want active. So, if OP wants the logo gone, they need to erase it from the color version (by copying the same brownish texture over it) but ALSO need to eliminate the grey scale.
I was editing the corkscrew model, and found that if you make a region solid black, it will allow the corresponding portion of your "color" texture file to be 100% dominant. I'll post screenshots when I get home, as it's a bit confusing.