What's the best way to do all this on a large PHP-based project?
The million dollar question. And the answers will be about as unique and broad as there are developers. It will likely come down to your personal preference. I'll share what I'm using and you can take or leave the pieces, investigate, etc. Fair enough?
Have you ever considered SASS? I prefer SASS (Compass) over LESS. I wrote my own Ant build to automatically compile any and all .sass/.scss in my Eclipse IDE when changes are made. The build monitors updates across a project and makes an exploded and fancy indented copy for development/testing/troubleshooting as well as a compressed version for production. This way I just develop as normal without having to be concerned about using the "create new project" and "watch/compile project" features of these nifty tools. It's open source, on github https://github.com/teeaykay/SassCompassCompiler
version control: git
cache-control (cache busting?): Apache configuration ( fairly good read on how to approach this at H5BP: https://github.com/h5bp/server-configs/blob/master/apache/README.md )