You can charge Eneloops at whatever drain state you want. Yes, they're generally completely drained at about 0.9v (resting), but unless you're cycling cells you haven't used in years (to regain some capacity), it's not worth draining them to that level before recharging.
I just broke out some 4 year old Eneloops, still in their packaging, to do some testing. Cycling was able to recover about 5% of their lost capacity, basically back to the level of brand-new (about 1900mAh). i.e., First cycle only gave about 1800mAh discharge capacity. After 3 or 4 full cycles (drained down to 0.8v), they were reading 1900mAh.
Note that cycling isn't required in most cases. It's only when Eneloops have sat unused for several years that cycling may help. Otherwise, all you're doing is using up a cycle for no benefit.
Generally, after 300 full (or equivalent) cycles, Eneloops are only good for low-drain devices. Their internal resistance is too high for flashlights, after that. But they still have most of their original capacity; it's just that you can only get it by running them at low drain (100mA or less).
I have some very old Eneloops that I've used well-over a thousand cycles. They're absolute crap in flashlights, and they have to be charged with a dumb slow-charger (smart chargers won't recognize them). But they're still great in some lights I made with 5mm LEDs, run at 20mA or less. They still power them for over a week, almost as long as brand-new Eneloops. They also still hold their charge well, so they haven't lost their low-self-discharge. They'd be great in remote controls or clocks. Don't throw away worn-out Eneloops!
