The Upper Madison's flows are low, its running around 1000cfs with water temps around 36 degrees near Cameron. Fish are a little wary so throw small indicators and fine tippet if you can. Baetis are active subsurface, but cloud cover is needed for consistent action up top. Throwing two smaller baetis/midge nymphs has been good. If you see baetis starting to pop shorten up that rig. Those nymph rigs don't always need to be hugging the bottom. Stoneflies and worms will do the trick as well.
If you're dry-or-die, prospecting with a double dry rig can produce. A few october caddis are around so try a stimulator followed by a small BWO or midge. In the evenings or on cloudy days watch those soft edges carefully. Fish will be pushed up into real skinny water to sip those blue wings. Fall baetis are small, fish 18's and 20's and "fish the rise" by watching the general area where you think your bugs are, and setting when a fish comes up. Sounds crazy but it works.
Streamer fishing is always an option on the Madison and will turn on in the evenings. Browns are starting to become territorial, and on a nice overcast day the bite can be hot. Good time of year to upsize those streamers into the 5 inch range, with the rusty trombone being a great option with its ease of casting and larger profile.
If you're feeling adventurous, try dead drifting a small streamer on a nymph rig. Fish are more willing to move for a meal this time of year, so if your looking for quality over quantity this can be an easy technique to get that done.
Dries:
stubby chubby, Tilt-wing BWO, purple haze, buzzball, stimulator, film critic BWO
Nymphs:
Perdigons, Green Machine's, zebra midge, $3 dip, shop vac, wire worm, frenchie, split-case BWO
Streamers:
Dungeons, Sparkle Minnows, sculpzilla, Boogie Man, Double Screamer, rusty trombone