A Cap will only hurt if its not installed correctly. a Cap will not Discharge or use much energy it allways connected to a Battery, a BatCap is best but very pricey.
If your system Discharges the Cap and recharges it on startup the surge can hurt the system. The CAP is on Float when not in use and connected to battery, when used in trunk with Amp it will let the amps surge and draw power from battery more smooth. This Will still hurt the alternator is your drawing more power then your system will make.
I strongly suggest what I did and add a larger alternator, a G6 large case 200 amp can hold my 1800watt kenwood sub and 750 watt kenwood powering 4 6x8s and carputer..
with AC and Headlights.