Hope I can get this somewhat correct??? I've got an Xtar SP2 charger (2 bay) that operate as independent charging channels. I too always charge my batteries in pairs; for stacked batteries it is a must to treat them as a pair. I notice that when I put both of them in the charger, one side will turn green before the other, always the same side. Wondering if my batteries were different, I checked the voltage of the batteries coming off the charger and found that the slot on the left side always charged my batteries to 4.21 volts. The battery on the right side would only charge to 4.17 volts. Needless to say, I wanted my off charger voltages and battery conditions to be equal, so now when I charge them I only use one side of the charger. Seems like a waste of a slot! My cheap Trustfire 001 charger got it a lot better than that.
In short, I really don't think it matters which side you put them in, as long as the charge on the batteries is equal (most important if you are using stacked batteries). You may want to invest in an inexpensive (under $10 meter to monitor you pre-charge and after-charge battery conditions. Makes a person feel safer.
On charging current, never charge you batteries at a rate higher than their mah rating. In other words, a 750 mah battery should never be charged at a rate higher than 750 mah. If you are getting the WP6 II, I notice that it has a fixed 600 ma charging current. In that case, you should be okay with most batteries; a 10440 would probably be too small of a mah rating to use with this charger. That charger also shows 6 independent charging channels, in which case you can mix or match your batteries at will in this device.
