Although the fish will usually be at the edge of the strongest current, there will still be some current where they're hanging out. It could be reduced current, or it could be reverse current like in an eddy. Regardless, it is important to present your bait properly.
Keep in mind that river fish instinctively know that most of their meals are coming from upstream. Wounded bugs or minnows or whatever will be moving with the current in a downstream manner. Fish that are looking for something to eat will be facing upstream, so we will want to usually cast our bait so it's working in a downstream manner. That will appear most natural to the fish. Not always, but usually you'll want to work your bait so it's moving downstream into the fish's face.
As the water gets colder, the fish will usually go deeper. Again, usually but not always. When they go on an aggressive bite they might move shallow, but much of the time they'll stay in the deeper areas. And, when they're in those deeper areas this time of year, they'll usually bite also.
Jigs are good ways to catch most species of fish in the fall. Sometimes when the bite is tough a jig tipped with a minnow will be what it takes to catch fish. A Fire-Ball jig with a minnow is tough to beat. The short shank of the Fire-Ball creates more consistent hook-ups, and the quick attach stinger hook is appreciated when the bite is really tough. I always take minnows along in the fall. I keep them in a Frabill aerated minnow container. These containers will keep minnows alive for days, so even if I don't use them on this day, they'll be ready to go the next day or the next.
Most of the time a Slurp! Jig tipped with a Gulp! Alive three or four inch minnow will be your best producer. The Slurp! Jig is employed because it has a long shank hook that is perfect for fishing soft bait. Thread the Gulp! minnow onto the hook so it's right up against the head of the jig.
Fall is a great time to be on the water. The scenery can be outstanding and so can the fishing. For the next couple of months, get out whenever you can. With any luck at all, you'll find that fall fishing in rivers can provide some really good action.