Best practices for running ICs with 12V vs 5V rails
The best practice to deal with mixed power rails like this project is to leave the high-voltage (12V) for LEDs, and feed every IC from 3.3 or 5V using switching DC-DC converter. To save troubles with things like high-current loops, inductors etc, I would recommend "linear replacements" like RECOM or Murata modules. These modules are not cheap, but will save you a lot of efforts. eBay can also help if the budget is really tight.