I try to have the cells fairly close in voltage before connecting them.
This is easy with the MCPx, just fly them for a fixed time.
If they are different then the current will flow from the higher voltage pack to the lower voltage one till they come into balance. Some have said this current is not a problem, but I still like them to be close.
Can't help you with the charger question, all my chargers let me charge through the main power leads.