This is one of those areas that varies between operators and customers.
From watching my local railroad and talking to the old road crew ages ago, the process goes as follows:
A through freight will stop in the yard and drop off a block of freight cars. This block may or may not be in the order to be distributed and it's up to the local switcher and crew to sort that out.
Once sorted, the freight is then delivered to the various customers. Some of the customers receive a regular delivery such as the perlite processor in the industrial park that got 100s of covered hoppers weekly while the warehouses nearby received a boxcar or two once a month. The brewery received a combination of the two along with some tanks for gases, hoppers for the barley and wheat, and boxcars full of bags of yeast. The bread bakery also received covered hoppers of flour and boxcars with yeast.
The way the drop offs were done varied between customers with many having trailing-leads off the main so that the freight could pull forward and drop the freight on the sidings. For the stub-ended industrial park branch, there was a runaround track part way down the branch so that the locomotive could go to the rear of the train to pull out the empties and put in the full cars.
If you want to see this in operation, watch some of the videos by Distant Signal.
Distant Signal - YouTube. He did some videos on local operations where he's located in Florida.
My variation works like this on my Gloucester Terminal Electric route. This route is divided into three operations with two of them fully automated and me taking over the third. The AI drives the through freights and commuter trains along with the trolleys while I handle the local freight to the various customers. I have a number of freight cars in the Gloucester yard along with many of the same scattered throughout the route in various locations. In some areas, there are locally stationed switchers such as down on the docks and also at the granite quarry.
After gathering the necessary deliveries, whether they're empty or full, the "road freight" goes out on the line to deliver goods and pickup empties. The trip requires careful timing between the trolley runs since the trolleys run frequently early in the morning with a lull just about at noon, the freight makes his journey then. It so happens that it takes about 2 hours to ready the consist, so the timing is perfect for this. He'll take the loop down to the brewery where he exchanges with the Riverside Railroad. The R&R is a shortline that serves the brewery and a "stuff" manufacturer located on the line. This is a short switching operation on tracks that have seen better days.
The hand-off is done here with a bunch of boxcars, hoppers and tanks, and the same are picked up. The empties are placed at theend of the train while the ones for delivery are placed on the end. Once hooked up, the freight proceeds and has to cross the Western Avenue trolley branch. He runs a short distance down the line and take the dock branch where he does his delivery to the small yard there and picks up and drops off more. There's a switcher here to handle the actual docks, so there's no need to switch the docks himself. After his job there, he proceeds on his own tracks along the waterfront to the State Pier where he drops off and picks up some oil tanks and reefers. The reefers are generally filled with frozen fish and seafood going out and empty going in. Once delivered, he continues on home rails until he reaches a good-sized yard and more docks where he exchanges freight before heading to the end of the line. The switcher mentioned previously handles the switching here as well.
The quarry is handled by its own railroad that brings its loads down from the quarry to the stone processing plants. This is actually two different operations with one being a stone crushing plant associated with a cement and lime operations and the other for marble and granite blocks. The cement and lime products are sent out in covered hoppers and the blocks are loaded on flatcars. This is all brought down to the large dock yard where the loads are then brought back to be interchanged with the mainline.
Sometimes, I'll throw in a twist with the mainline freight will deliver or pickup freight cars. This involves me taking control and driving the freight into the branch where he drops off and exchanges cars at the wye before continuing on his way to his destinations. This switching operation can run up to eight-hours or more when the AI behaves which is most of the time. The action can get a bit hectic as I have to avoid the trolleys which have priority over my local freight. In case you're wondering, none of these interactive industries and it's all played out in my imagination. For open loads, I'll edit the consist and add in visible loads by editing the session in UDS. This is where the old consist access was great as Phil Skene and the others wish we still had.
In the end, it's up to you to work out the best way to handle your customers on your route just like the crew does in real life. Given that there are so many variations of this, you can pretty much do what you want.