You are going to have to give your application/IIS "write" rights to your CSS file on your web server. You are then going to have to write code in your application to physically change the file. That said...
DON'T DO THIS!
If you need to modify your site and don't want to dig into the code each and every time, use a well known and thoroughly-tested CMS. Writing your own code which gives users of your site write access to its files is hideously dangerous. You can be guaranteed that there will be security holes that you don't think of and in the end some hacker will make you pay dearly for your mistakes.