make sure you mount the capacitor as close as possible to the amp(s) for greatest efficency... use a seperate ground, not the amps ground, but ground them to the car at the same point.
As far as charging it... being sure the fuse at the battery is out, connect everything properly first... then once everything is connected, jump the 2 terminals of the fuse holder with a small 12 volt light bulb... a test light works well... keep it there till the bulb goes out, it might take a minute... once it does, pop the fuse in and you should be ready to go.
You can also connect everything but the power lead from the battery to the cap, use the bulb between the power wire and the positive terminal of the cap, again untill it goes out... I just find its easier to get everything done first, then charge it at the fuse as the last step.