I can give you a tip on how to maintain control of long stretches of river as the Union[SUP]1)[/SUP] at the least cost in nerves[SUP]2)[/SUP]:
stack 2 gunboat squadrons (2 gunboat elements each) with 1 riverine transport squadron (4 elements--I have no experience with 2 element riverine transports) together into one patrol, then post them somewhere along a stretch of river you want to "control" in Defensive Posture. As long as their transports can draw supply along the river or from some local harbor your patrol-squadron will stay in business.
They may take some hits in winter from storms, but I've had the entire shippable Cumberland River plus much of the Tennessee and lower Ohio Rivers blocked throughout a summer and winter without having to pull a single patrol squadron off from weather damage or loss of cohesion.
As long as they are not sailing up and down the river from one river region to another, they will use relatively little supply and take little Wear-n-Tear™ and rarely lose cohesion.
[SUP]1)[/SUP] I'm not sure the parameters for CS patrols as they have their own supply capacity and might get by without having riverine transport in each patrol squadron, or maybe only interspersed every other patrol squadron. The CS usually doesn't have the gunboats to patrol more than selective parts of the river at selective times.
[SUP]2)[/SUP] I don't expect there to be any major changes in how patrolling/blocking-crossings work.