I'm with KK on having three rods set up. Mine would be a floater, clear intermediate and a type III full sink when I'm using my SFC or pontoon.

In my raft, I'll add another floater so I can have both a chironomid and dry fly rod rigged and ready. Each lake fishes differently based on the time of year, depth, hatches, water temps etc. The lake I've been fishing lately has required nothing but floaters to get the job done.

One other line that works really well is is a type VI full sink. Great for trolling deep lakes as well as vertical chironomid fishing.