Never store batteries fully charged. Charge them, and run them soon after. If you're not going to run them, put them back into storage mode. I set my low voltage cutoff on the ESC to no less than 3.4v per cell if possible.
Plug the battery in. Select the channel you plugged into. 1 is on the left, 2 is on the right.
Press the scroll wheel.
Select charge
It should automatically detect the cell count, but make sure that matches your battery - 2S or 7.4v.
The charge rate will be the mAh of your battery divided by...
You can use a 6S balance lead for all batteries up to 6S. You just have to remove the tab from the connector that prevents the other batteries from plugging in.
Here are a few of the various adapter cables I have made up for some of my batteries...
And here is how I modified the balance...