Terrence:
To start with you generally ciscoes relating to the open basin most of the time during this seasonal period and finding them is generally going to happen off mid-lake structure in the basin. Once fall starts to come closer, I have found that they will start to move closer to spawning locations holding at approx. half the depth of the bottom. They are not generally dependant on the thermocline. They will die if the water gets to warm.
So for pointers to chase, I would troll some type of system that gets ya in to 20′-30′ of water as the gamefish generally will not be deeper than the thermocline. You can/could use snap weights, dipsy divers, leadcore or even down riggers to do that. While trolling now you are looking for the baitfish to become you structure. So start making laps in the basin with bait low and if ya have si or sidescan be looking for stuff off to your sides as well.
Once located you could try other type of fishing methods.
More questions let us know…
Mark