All in all, I'd say that you'd want to implement a generic timer system for all of your commands, along the lines that each player should have the same chance of doing something, regardless of connection, or if they're using a third party program to play them game.
Since I don't know anything about your game I can only make general comments, but it sounds like you may want to implement the concept of a "round", where only one action, like a movement or an attack, can occur from any one player. If you do this stuff now, you may be saving yourself some headaches later on. I think its always better to put things like this in at the begining instead of trying to bung it in in the end. That's why most game development projects never make it to the end.
More importantly, what's this game all about, and when's it going to be done? 😉
Erestar