You might find some answers on the porch & deck forum.

Epoxy will deteriorate with UV rays from the sun, and if you get it on the flag stone it will not come off.
What I have done is to first grout the stone with masonry cement lower than the flagstone. They sell a grout bag at most Lowes, Home Depot's and Lumber yards. They work well for this. While the mortar is still wet push the pea gravel into the mortar. Let it set for a while, until the pea gravel is holding. Then wash it with a water hose. When it is dry Wash it with a cleaner designed for the purpose.
I would advise that you practice first before doing something permanent on the entire patio.