I think it depends on what you want out of it. If you just want a user to be able to choose a theme for your site, maybe consider inserting / swapping out a <link> tag depending on which theme the user has chosen? Then just save the theme they have chosen somewhere (possibly on a backend, or localStorage for client side) and do a check each time they load a page and insert the chosen theme's css file.
If you want them to be able to change values (e.g background color, font color) based on their input and have it save specific to them, you might be out of your league a bit based on your question. However, if you're wanting to attempt it, try having a <style> tag on the page and swap out the values based on user input. Keep in mind, this example is just a super basic option for implementation. There are better ways to do this.