Well, you pretty well spec'd it out for mechanical arrangement. The next question is what are you modelling? Part of a main line? Branch line? Interchange or bridge route? Is it point-to-point, folded dogbone or what? Are you running main line passenger trains, commuters, mixed train locals? What is your location? Do you have grades to contend with, or mainly flat territory? Are you running DC or DCC? How many operators will you have at a time? What sort of industries do you plan to have? Will you be running raw materials to a factory and finished product from the factory to a destination on the layout, or will the finished goods be transported "off the bench"?
For example, I have a small farm at one point on my layout. I have beef cattle which the farmer carries to loading pens. This is on a branch line. A couple of stock cars carry the cows to a nearby packing plant where they are processed. Processed meat is loaded into ice bunker 1950's era refrigerator cars, which load ice at an icing plant next to the packing plant. The refrigerator cars go to the other side of the layout to a Kroger food distribution plant. "Empty" refers go back to the packing plant area. Near the farm, but not right next to it is an open pit coal mine. Loaded hopper cars are hauled to the classification yard, where they are picked up by either a pair of SD-7's or a Burlington M2 2-10-2 or an M4 2-10-4 for a trip up a steep grade and "West" to a coal-fired electricity-generating plant. Cars are pushed in behind the plant to a grade that runs downhill behind most of the visible scenery, where they emerge back at the tunnel from whence they came originally. They are switched out of the way, and a block of empties are then pushed up the hidden grade, emerging from behind the generating plant for a trip down the visible mainline back to the mine, as though the loaded cars were emptied at the plant. I also am working on a sugar beet processing operation, where the same farmer dumps beets that are loaded into a hopper which is then taken to the processing plant. Processed grannular sugar and molassas are taken from the plant in covered hoppers, in sacks loaded in boxcars, and liquid product in tank cars. These are transported down hill to the classification yard where they are sorted and then sent back uphill to a merchandise building.
Continuous running is possible on my folded dogbone layout, and you may see the Denver Zephyr, the Empire Builder and the North Coast Limited or pooled trains, depending on my mood and what guests want to see run. If it is 1948, you will see President Harry Truman's "Whistle Stop Special" come through, with Truman and Bess and an aide on the back of the Ferdnand Magellan. At Galesburg, Illinois, a crowd is starting to gather, mostly passengers from the sidetracked Zephyrs. A man holds a six-year-old boy on his shoulders. Even though the man is a staunch Republican and will vote for Gov. Thomas Dewey, he wants his son to see The President. Sixty-four years later, I can still see and hear Harry giving 'em hell as we stood there!
Point of all this is that you need to have a story in mind or several. If I can figure out how to do it, eventually I will try to post some photo vignettes.