The EM Knight challenge does not consume stamina and your troops may be healed in your headquarters. The best strategy to destroy the EM Knight is to focus your attack on the batteries that surround the boss. Basically the more batteries that are destroyed, the more damage the EM Knight will sustain. Attacking the batteries will cause the EM Knight to become vulnerable to direct attacks. You will recieve rewards for each of the three allowed attempts on each level of EM Knight.
The Level 1 EM Knight batteries must be attacked three times before they are destroyed. When the Level 2 EM Knight is summoned the batteries hits moves to five times before they are destroyed. This means your three attacks will take out 60% of a battery and will require another corps member to attack the remaining amount to eliminate it.