Unfortunately you cannot just connect them in series because of two effects. The first is the tolerance in the value of the capacitance. A +-20% variance is normal in capacitors (it could be bigger or smaller depending on the specific model). If one of your capacitors is 500*1.2=600F, and the other is 500*0.8=400F, then the voltage across the first will be 2V and the voltage across the second will be 3V, which will damage it and or make it explode.
The other effect is the leakage current. All capacitors have a leakage current, and on supercapacitors it can be quite large. If one capacitor leaks more than the other, which is pretty much guaranteed to happen, then the voltage on the one that leaks less can go up, possibly going above 2.7V and damaging the capacitor.
You could use resistors to deal with these issues, but the current required may be quite large and unacceptable (usually it should be at least 10X the maximum expected leakage current). You could also implement some active circuit, and there is more info here