Since the Canon NP-E3 Battery Pack is NiMH, care must be taken to maximize battery capacity and life. Ni-MH requires less care than NiCad batteries, but is not as care-free as Lithium-Ion batteries.
Chuck Westfall, Assistant Director/Technical Information Dept for Camera Division/Canon U.S.A., Inc., recommends running a brand-new Canon NP-E3 Battery Pack through 3 or 4 complete discharge/complete recharge cycles prior to normal use (or during initial usage). This procedure will maximize the battery's capacity.
The Canon NP-E3 Battery Pack discharge/complete recharge cycle done on the Canon charger takes about 8.5 hours for the discharge cycle plus about 2 hours for a complete charge. Overnight is a good time to do this - 10.5 hours is a long time.
Chuck Westfall also adds further advice for professionals - a professional generally meeting the following profile: Owns 2 or 3 batteries, uses their camera at least 5 days per week and averages at least 1,000 shots per week. The Canon NP-E3 Battery Pack maintenance recommendation for a professional is to recondition each battery about once per month after the initial conditioning.
Chuck also stresses that this is a guideline - not a requirement. Individual shooting styles may dictate adjustment from this recommendation.
My recommendation is to have at least two Canon NP-E3 Battery Packs. Keep one in the camera until fully drained, keep the other(s) fully charged in your bag - ready for immediate use. You are basically giving each battery a complete discharge/charge cycle during each use.