With how node.js influenced frontend dev is those days, looking for index files is good way to start. The entry file to Misago's styles lies here. To customize your CSS you'll need to clone Misago's frontend somewhere and edit gulpfile.js's var misago to point to theme/static/misago directory. theme directory is created together with rest of files when you run startmisago.py, but you'll need to create misago dir within theme/static yourself.
Once this is done, you can run gulp watchstyle that will watch less files for changes and will rebuilt theme/static/misago/css/style.css if any of them change. If you are pleased with results, run gulp style which will build minified style.css that you may deploy on production. If you want to add static files like images, you may drop them in theme/static as well and they will work too.
I'm currently working for default theme for Misago, and eventually I'll love to improve and document process of writing custom themes for forums, but for now cloning and modifying frontend is best option.