It kind of depends on what kits you're planning on using.
If you're talking old school style marines and chaos,
GW used this method for the 13th Company army back in 3rd edition in the Eye of Terror codex. It's a great look, as the two kits were designed to be interchangeable.
Newer chaos kits should still work with the old school marines, but it will take a little more hacking to get them to work. If you're wanting to avoid overtly chaotic symbols, you'd be better off using the old style chaos marines anyway (and they're probably cheaper).
It's a great effect, and I whole-heartedly encourage your project!