the way i read it when i googled it, was the power cable comes from the battery to the + terminal of the cap, then to the power terminal of the amp... then you just ground the cap, which i'd probably ground at the same point as the amp.
Not sure about my alternator... I died right after I got the car... guessing it was replaced w/ a stock type alt. I've been meaning to go junkyard hopping lookin for a 3g or just buying a refurb.
What size amp and subs are you pushing? Chances are you just need a stronger alt. that won't die like a cap will. I personally don't like the star trek lights of caps.