gotop ships with a few colorschemes which can be set with the -c flag followed by the name of one. You can find all the colorschemes in the colorschemes folder.
To make a custom colorscheme, check out the template for instructions and then use default.json as a starter. Then put the file at ~/.config/gotop/<name>.json and load it with gotop -c <name>. Colorschemes PR's are welcome!
To list all built-in color schemes, call:
gotop --list colorschemes