I've seen people track it with Cmaster as Keith suggested by using three colored dot markers. I think they did green for action, blue for bonus action, yellow for reaction. Remove the appropriate dot as action/bonus.and reaction are used. At the start of each turn Cmaster automatically applies the three dots to the token if they are not already applied, thus replenishing the action set. If you use lots of token markers for lots of conditions this gets a little busy looking because its using up three markers on every token. But if you don't use a ton of markers it works like a charm.
