I have fished with "fly bobbers" for 40+ years on lakes/rivers/streams and have a few observations of my own to share.
I have been very successful even when the lake surface is like glass which is the hardest time to catch anything in those clear lakes.
Use a long and light leader. 6' min. for me and 8' isn't too long. And generally a 2 lb. leader. Big end of the bobber goes towards the pole, not the fly. Use clear bobbers.
Cast out as far as you can when you are "searching" for fish and just before the bobber gets to the water, crank the reel enough to set the bail and then pull back on the pole enough so that the bobber starts to come back to you just "before" it hits the water. That causes the leader to straighten out and the fly to land behind the bobber in undisturbed water. (takes a little practice). Let it sit for a minute before starting the retrieve, but be prepared as many fish hit while you are letting it "soak".
Retrieve slooowly (lakes) and stop from time to time and "twitch" the bobber a little to cause the fly to move just a few inches. With a slow retrieve you will leave no ripples on the water. (Rivers and streams you can retrieve a litte faster, just don't drag it faster than the fish can catch it)
Fishing targeted rises, cast just past and bring the fly through the rise using same technique.
Just before lifting it out for the next cast, let it settle for a moment to make sure a trailing trout has one last chance.
I have found best luck overall with wet flies like yellow or black wooley worms and similar patterns with a taste of red at the tail or black ant patterns. Dry flies on lakes work, but its easy for them to get pulled under by the dragging and then they are no longer floating and fish seem to not like em then. Fish them even slower so they basically are sitting still.
The way I fish lakes, the retrieve may take 4 or 5 minutes/cast (longer with dry flies, but I tend to wet patterns). You can set the hook a little when they hit, then just make sure they don't get slack line.
If you expect bigger fish, set a light drag. Anything up to 12-14" should be no problem on 2# leader and larger fish are fine if you don't lock em up to hard with the drag. ( I once caught and landed an 18# salmon in the fast water of a river on 8# test line, just took almost an hour and a fair amount of patience)
I have used a fly bobber successfully with a bait hook and an impaled cricket, grasshopper and salmon fly as well, and fished pretty much the same way, esp. on moving water.
Don't forget that this same setup works for drifting flies (and bait) around on streams and rivers as well (on smaller streams/creeks you may want to shorten up the leader to around 4' or so, then its easier to "steer" the fly with the bobber). A fly bobber setup can be very effective and the spin gear provides lots of versatility that you won't get with a fly rod only.
Anyway, works for me...hope it helps ya. Good Luck all...