ya stacking can be a bit tricky. to start off, you need to make sure you have enough space between your stacked lines. that mostly depends on trolling speed, whether both rigs have flashers, and cannon ball wieght(i use 10's cause i have handcranks - definately use more if your using electrics). if i'm trolling my regular speed, and have a no flasher rig on the bottom and a flasher rig on the top, i'll stack them 22' apart. if they both have flashers, i'll push it to 30'. if neither have flahsers, i'll go as close as 12'. some people get away with stacking them closer than i do, but i don't think its really necessary and you'll get tangled more. also, make sure you stagger your depths in relation to the other side of the boat. say you want to run four lines and you know there are fish at 60'. run at 44 and 66 on one side and 55 and 77 on the other. that way you are all around your target depth and all your lines are reasonably far apart.
when you hit a fish, what you do depends on what it is. if you think its a spring, by all means, get all your gear up. if its anything else, sometimes with the exception of big chum or big coho, maybe just slow down a little but leave the other rods down. except if its on a bottom rod, then get the top rod up as quick as possible. most tangles, in my experience, are from coho grabbing the bottom rod and heading for the surface. if i see something hit the bottom rod, and it doesn't pull it out of the clip, or look like a spring, i'll pull the top rod off the clip and get someone else to real it in, or put it in a rod holder on the other side of the boat, or whatever it takes to get it somewhat out of the way, then deal with the fish.
my advice is not to run too many rods unless you have enough people to deal with all of them, or the fishing is slow and its necessary to catch something.
if fishing is reasonable, i'll start pretty much every morning with two rods regardless of how many people i have out, then as it slows down, throw out a top rod, usually a hootchie or a big whole herring. and if its dead, put out the forth.
hope this helps, but this is just an opinion, i have only guided 2 years, there are ppl on here that have been doin it alot longer than that who i'm sure have different ways of doing it.
Thanks Captain Dudds