In a given chronoamperometric experiment, the amount of charge can be obtained as the integral of current from t=0 to t=t (time of polarization at a given potential).
For a capacitor, the capacitance (C) in Farads C = Q/V where Q represents the charge in Coulombs and V the Voltage in Volts. Then you can infer that Q for a capacitor (integral of i dt, from 0 to T) = C V = Q.
Now, assuming that you recorded the voltage through time and that you seem to have the capacitance through time as well, you can then easily have the charge. Normally, the calculation of the integral is pretty much straightforward. If you would not know how to do it, I recommend that you save your data in excel as "tab delimited text" and import them into a software such as EC-Lab from Bio-Logic. You can donwload a demo version for free from their website. Once you have imported the data there, you simply select the whole series, click on the meny Analysis>Math>Integral, and the value will be immediately displayed. Make sure your data are in the right units.
Now, that is for the calculation of the total charge. To derive what is the electrochemically active surface area, you must know the processes contributing to it (e.g. diffusion as the limiting step, adsorption, etc). You may find a good guide for that in our paper from this year in Electrochimica Acta. Although it was meant to explain bioelectrochemical systems mainly, it very well applies to any other field. If your system is limited by diffusion ALONE, then you can determine the electrochemically active surface area by Anson equation. Yet, if there are other processes contributing, such as a large capacitance from the electrodes, adsorption, etc., then you should be very careful on how to estimate it. I would say it is a difficult calculation unless you know well your system.
Please note that our publication has an error on equation 3 that has not been corrected by the editorial. It is not a big issue, you may use the first part of the equalty but not the last part of the equalty (the current was placed instead of charge).