Can you simply add the color flakes with the clear?
Short answer - yes.
Our BondTite 1101 is primarily used as a primer, but it's also used as a top or clear coat.
The flakes are broadcast on top of a fresh, still wet, coat of BondTite, then another coat should be applied to seal in the flakes.
Depending on the type of punishment the floor will see you may need more than the one coat, if you'll just be parkng cars a single coat may do just fine, but if you're going to be wrenching and/or doing other physical work you may want to build up the epoxy to handle the extra wear and tear.
Also if there's going to be significant UV exposure a polyurethane clear coat will help mitigate yellowing.