In case I only answered half of your question, let me also clarify what the Base URL and Base Path options are in the Advanced Preferences pane of Minimee…
These two values help Minimee find the *original* CSS and JS files, i.e. the files that Minimee needs to fetch, minify, and combine together before saving into the Cache Path directory.
I’ve made Base URL and Base Path available in case your CSS and/or JS files are not located in an obvious relative location to your main EE index.php file (e.g. http://johndwells.com/index.php is mine). So for example if you are running EE at a subfolder, say http://juleswebb.com/ee2/, but your CSS & JS files are below that, say http://juleswebb.com/cssandjs/, then you’ll need to specify that in your Base URL and Base Path.
You’d also want to do this if running MSM, but serving all CSS & JS assets from one location.
Again, I hope that helps. But please do post some sample code if you’re still having trouble getting Minimee to find your CSS & JS files…