I use the putty, but only a wee bit, just enough to barely coat the line and, umm, serve as an indicator. I only use it for deep nymphing for smallmouth where a lot of the takes are pretty subtle or bluegill-like. Often as not, the putty section of the leader is underwater, but close enough to the surface that I can see it and react if it makes a funny move. It helps...
When I was fishing Wisconsin, I usually nymphed for trout with a tandem rig and a small Thingamabobber. Now that we're back here, I've gone back to a single nymph and no indicator for the most part. Unless I am fishing one of the limestones or for bigger water stockies (Oil Creek, etc.), when I'll go back to the tandem and small indicator. The difference is about stream types and fish density. In the usual PA waters I fish these days, both these factors argue against putting up with the aggravation of a tandem rig and indicator.