If you're running components that require a 50f Capacitor then I would say you're probably taxing your electrical system just a bit and the HO Alt. is not going to hurt. You've obviously spent some cash on the stuff, it just might require a little more.
Have you load calculated your current/power draw from all you have installed, including the lights? Although I think the lights are the least of your worries unless your dimming only happens when you have the lights on. Without really knowing what kind of power you need at full load we're all only guessing here.
Lol... Have you considered a LARGER Cap? hahahaha, that boggles my mind to need something so big but they DO make them. The HO Alt. with 2nd battery set-up, larger cap might be what's needed here, isolating power to the added components on their own power grid!

Just my $.02
I forgot to answer your question...
Yes, relays can be added if that's what you want to do.
The relay's act as switches, controlling the power going out to the device you want to turn on/off. The power line that is controlled by the relay can be from either the stock wiring or what is better is taking the power direct from the battery or fuse block. There are some set up's I've read and it is all a bit involved to do it right but not difficult as long as you do your homework first, lol.
Check this out... might help some...
http://www.backinblackgp.com/