Charging to lipos that are the same qith the same charger from storage if one takes 3900mah and the other 3500mah which would be in better condition?

I'd run them both!

Ideally you want something to test the packs internal resistance.

Both packs perform fine and seem in great condition i just wondered what the difference is mah from storage might mean. What can be used to check internal resistance?

Some chargers can measure internal resistance (I know my Graupner Polaron does) but I find the most accurate is a resting IR reading from a pack that hasn't been used for a while (15-20 mins) using one of these:

http://hobbyking.com/hobbyking/store..._IR_Meter.html