just because a company states its 4gauge doesnt mean it is.. look at the cheaper brands on Ebay and then compare to quality brands.. the difference is in the strand count of the wire.
also, i would ditch the capacitor.. lets take a moment and think about our electrical system? ok.. lets say you have a totally stock stereo, no aftermarket amp or anything.. lets say at idle, your voltage is 14.5v, well, lets add your aftermarket amp to the car, well now we are losing voltage because its an electrical device that demands an X amount of current.. your car will never give a piece of electrical equipment too much current, it will only take as much as it needs, which may be a 3 or so voltage difference.. so now with your car at idle, lets say its 14v. you lost .5v which is a big deal, lets count whatever the car has to power, the windows/locks...etc if it has that.. well you have your ac/heater, turn that on and you may lose more voltage.. so now you add your capacitor because the guy across street has one and says its the fuckin bees knees and will solve alllllllllllllllllll your problems.. Wrong. that capacitor is more or less a band aid to your stereo. it will hold a single charge for one bassline and will have to recharge after that, pulling more current from your alternator, along with the amp and power accessories in the car already.. the capacitor is Not going to make a difference(although cap vs no cap is an on going battle, its really up to you)
there are four terminals on your sub because it is a dual voice coil sub, do you know if it is dual 4ohm or dual 2ohm? it should say on the sub somewhere, or could you give me the model number? and what amp are you running? i believe you said Boss Audio? im sorry to say but that Boss Audio amp is not going to put out the rated amount of power it states. those amps are cheaply made and will give you poor results.
oh and yes, you could just look at the meter on the capacitor to tell you the voltage.. whats the voltage with the car on but the stereo and everything off? and then turn the stereo on to your normal listening volume and whatever else you would normally have on, and let me know what they are.. if your voltage is below 13v constantly with the car on, with/out the stereo on, you have an electrical problem and your amplifier is working harding to pull the current it needs to supply the power you want from it, thus creating a clipped signal, which is initially what fries amps and causes voice coils in the subs to fry.
also, whats your amp grounded to? it should be grounded to bare metal, best place would be the Frame of the car. not the tire bolt in the trunk or some shit. you want BARE metal. sand down the metal spot and try it out.
here are a few pictures for reference... if you have a single sub and it is a dual 4ohm sub the lowest you can wire it is a 2ohm load, to achieve a 2ohm load you would need to wire your sub like this:
the sub in the picture is wired in parallel, creating the 2ohm load.
if you have a dual 2ohm sub, you can wire your sub for a 4ohm or a 1ohm load.. (a 1ohm load on an amplifier isnt something all amps can handle, as you pulling more current at this state. if you cannot provide sufficient current, you will have problems, like the amp getting very warm and going into protection, eventually it will fry the internals).
for a 4ohm load you will need to wire the sub in series like this:
and for a 1ohm load you would just wire it in parallel.
so give me the model number of the amp and sub, and we can go from there and start the elimination proccess the right way. one by one. you may have the amp wired too low of a load.