Hi Tie one on,
I'm pretty much in the same climate zone your at, I live in Northern Minnesota. Right now is my favorite time to be chasing bronzebacks in the rivers, they are starting to school up more, but still stay fairly close to feed as they gorge on prey for the upcoming winter months.
I looked back through my logs and I've caught smallies shallow all the way through October, albet a little chilly and fishing during bankers hours 9-3. There have been Minnesota DNR studies that show some smallmouth stay 3-4ft all winter long and some have even migrated 32 miles to winter. Now I know studies have alof of variables, but still interesting. If I was to generalize when I it gets tough to fly fish for smallies, I would have to say when the small puddles or shallow roadside marsh areas start to get a little skim ice on them. To me this is when many of the smallmouth have started staging into their wintering areas, water surface temps might be in the upper forties during the day. Like anything else alot depends on the weather, because sometimes we do get warm spells during the fall, which can get the smallies real active again. Minnesota October's weather can real unpredictable.
I've only found one wintering area on a local river that I fish. I had put the fly fishing gear away and was out fishing for some late season walleyes vertical jigging with big minnows in a deep hole. But after catching smallmouth in this one spot, I examined it real carefully to find out why they would be here. First there is a long shallow rocky flat up river about a 100' yards long with scattered big boulders averaging about 5 feet. I've caught many smallies during the summer months in the same area. At the end of this flat was a significant drop off to a deep hole about 10-15 feet. Got the camera out and it was a muck bottom with a few smaller boulders strewn about and timber mixed in as well. Of course we saw the smallies swimming around, not a lot (probably because the stained water and the camera down there), but it was enough to know that they were stacked in there. To me it didn't seem like there was a huge amount of current flow below the drop, like most of the current flow stayed near the surface, which is probably what the smallies are looking for to spend most of the winter. I'm not smallmouth expert, but it's a good theory. There is a reason why Minnesota has a catch and release season on all smallmouth starting mid september, thats because of the schooling nature of smallmouth during the fall and aggressive feeding during this time. It's the only fish to have an early C&R rule during the general fishing season and it's actually helping.
I've tried to break out the fly rod using some sink tip, but have never caught anything. I think I might have to using full sinking line, but that will still be tough because of the upper sections of the river still have some current. So you have to get past current, plus get your fly down to the bottom, not an easy feat, but could be done. The ones I've caught using a heavy jig and minnow have been light taps or slight pulls right near the bottom. I know there many other deep holes in this river system, but only seen them stacked in this one area, but probably because we don't do alot running during late fall and the short fishing window.
Remember this is just my observations, but I'm sure it's different for each river and water system. Tight lines and good luck out there.
Here is link to couple articles about the research:
River Smallies.com - Smallmouth on the Move (Eric R. Altena)
Minnesota Conservation Volunteer: Field Notes - Smallies on the Move: Minnesota DNR