Can you spend both energies on the Protons to get two crits? and if you are running fail safe munitions does it have limited uses?

1) No. You spend the charge to be able to perform the attack. In performing the attack you may change one hit to a crit.

2) You may use munitions failsafe as many times as you can fire your missiles or torpedoes. However you must use it before rerolling or modifying dice (through a target lock or a focus).

About the only time you would even consider using it (outside of a few janky uses on a couple scum pilots) would be if you shoot a missile or torpedo, entirely blank out on the initial roll and decide to save the target lock to try again later.

For Proton Torpedoes , spending a charge is part of the cost of performing the attack itself; it doesn't generate the hit-to-crit effect. That effect is an automatic (and coincidentally, not optional) thing, that happens as part of the attack. It happens only once per attack, and can happen at any point during your dice modifications (so if you happen to roll all focus results, you can spend a focus token to convert to all hits, THEN modify one of them to a critical hit)

Munitions Failsafe falls under what I call "safety net upgrades:" things you add to a ship to give you a small bonus if things don't happen to go your way. Composure is another; designed to at least give you a focus token, if you fail a different action. Most of the time, those upgrades aren't that effective in competitive play, outside of occasional janky combos (like Torani Kulda, R5-TK, and Cluster Missiles), but it's a nice way to spend an extra point if you have nothing better to do, and don't want/need the initiative bid.

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17 hours ago, missileaway said:

2) You may use munitions failsafe as many times as you can fire your missiles or torpedoes. However you must use it before rerolling or modifying dice (through a target lock or a focus).

To clarify, If you want to use Munitions Failsafe, you have to use it even before your opponent modifies your attack dice.