Recharging dissimilar batteries
If your charger literally must have a pair of slots occupied to charge then you should probably retire it. This suggests that it probably (not certainly) charges the pair in series. If this is the case then significant reduction in battery lifetime can occur OR one battery may be grossly undercharged, depending on the charger end point decision method. Chargers that work in that manner are usually old and or cheap (and if not cheap, should be). Eneloop batteries are excellent products with long cycle lifetimes and low self discharge and deserve to be treated well. 

I'd recommend a decent charger. Look at the candlepower forum pages for ideas on what is good and good value. I uses a "Maha", "Wizard one" charger and find it excellent. They are dearer than some alternatives. You'll never regret owning one once you forget how much you paid for it :-).