Your link doesn't work for me.
What I do for layout design (have done so far) is define my area and benchwork first. Next I decide on a theme. (Mainline running, with a branch line(?) or other special interests.) Then I put in a mainline. I am fond of twice around the room types divided by scenery and grades.
Since I have gotten into operations, I also have a staging area of some sort, whether it is a lay-over for entire trains, or a yard that simulates an interchange yard. One track in staging is a through track for continuous running. If I put cars on it, the layout becomes point to point for operations.
Next I try and determine how many small towns I can have, and possibility one city with a yard and loco facilities, without them crowding one another. Usually small yards and facilities unless I have the room for larger ones. I will try to fit in a way-side industry or two just for variation as long as it won't crowd things.
Then I go looking at plans for modular railroads. I look for ones that would make good towns or cities because their track plans are usually fairly compact, and most of the way they will be switched is already determined with a good track plan themselves.
Because I freelance, I don't worry about town and city names etc., but if you want to model a specific prototype, you can name the towns as the railroad you are modeling would, and build or plan you scenery to suite the area you want to model. Also, some of the industries that may be recognizable in a town you choose to name from a real one may have to be built or otherwise implied to achieve the "feeling" of the real town.
When building starts, I try and get all of the benchwork built first. Then plan where the towns will go and install the mainline to get some trains running. Then I work on one of the yards so I can store stuff when not running. Then I plug along on the other track work and scenery design and continue from there.
Hope this helps.