If I have two 3s 11.1V 5400 maH 20c batteries wired in series will the combined batteries equal 40c's? Iam probably posting this in the wrong area, but I am new to this. I want to run the two batteries in a series on my T-rex 600esp.</p>

They are still 20C

In series that makes a 22.2v 5400mah 20C battery
20C * 5400mah / 1000 = 108 amps max sustained current w/o hurting the batteries. (thats a LOT)

hmmmm....So, wouldn't it make it 10800 mah, combined, for longer flight time? and 20C is kinda weak for a trex 600, no?

And how do you figure the 108 amps?

He showed you where the 108 amps came from. 20C * 5400mah / 1000 = 108 amps.
When you put two identical batteries in series you do NOT double the mah available, you double the voltage present. In your case with two 11.1volt 5400mah batteries in series, you would have in essence one 22.2volt 5400mah battery. The C rating also would not change.
But then, isn't that what BarracudaHockey said?

To double the capacity, you need to connect them in paralell. This would give you 10800mah, but you would still be at 11.1v.

Then, am i right to assume that a 100 amp ESC will not handle that setup? And how can I make my trex fly longer? I need to get about 20 minutes of flight time per charge?</p>

First you need to know the draw of the setup you have(MEASURED, Not Guessed) and then try to match the ESC and battery pack to get the flight times. You need to know that the heaver the flight pack(batteries) the more the motor will draw to lift them.

Cheers

You need to work out or measure the current draw of your motor at full throttle and max pitch. This will determine the size of your esc. If you connect the batteries in series you will have 5400mah at 22,2v still at 20C The "C" rate is the maximum available current draw of the battery and is measured in mutiples of battery capacity, for example a 20C 5400 mah battery would give you 108A maximum, as stated by BarracudaHockey. The C rate of the battery is determined internally by the construction of the battery and you cannot change it by connecting it in series or parralell. If you want a longer flight time you will need larger capacity batteries with more cells i.e 2x6s 5400mah batteries. You need 6s batteries to be able to sustain the 22.2V that the esc needs.