The capacitor is more to deliver the extra power needed when the amp and subs are working hard.
It doesn't stop the alternator from having to work its backside off to supply the power needed for the system to run, but it can help stop some of the peak spikes that the amp can require.
Think of the capacitor as a smoothing device, when the amp suddenly needs that extra shot of power for a split second, the capacitor is there to give that little extra. But it is only designed to help smooth those little spikes, not deliver a sustained supply of power.
You can look at having the alternator upgraded to a larger unit if the current one isn't supplying enough power, however that does become a bit of an engineering challenge, as usually you would have to get someone to make up a new bracket to mount the larger alternator.