The maker of the battery does make a difference, I myself have always suck with Anker, I have tried some cheaper variants but have always been disappointed.
Bottom line though, you won't find an app that will accurately tell the mAh rating, you will require a stand alone device to determine this. If you can control every aspect of the os and run a series of tests with each battery and determine life by use... I would start by returning to stock, going in to airplane mode then use a high power consumption app by itself from 100% to 0. Do this with both batteries, theoretically your 3500 mAh battery should last about twice as long as the stock 1750 mAh battery. Good luck
Sent from my SAMSUNG-SGH-I997 using XDA