I start by building in the vanilla spots, I've found some in very great spots. I either fix up the vanilla buildings or tear them down and build something smallish; As I'm running along finding these locations I'm also putting pins on the map of any POI and sometimes just pretty spots.
After doing this for a bit I then asses the map & also landscape to lay out some general dirt roads. The locations with multiple buildings I make towns and consider their roads more travelled.
After a while I end up with a kind of story for each location and spend more time building up some areas than others.
Here is my most recent map, not very far in:
ibb.co/W0DqKx9To the north is my trader, the starter houses a friend and I built are in the middle near a lovely lake. The southern big red circle is the major town/dock that I have just started on; it has a few houses going up the coast east. There are a few towns/farms near the mountains that I also plan to build out. My friend build their 2nd base to the far east in a tower at the base of a mountain.
Also, I don't use that portals list mod. I like to build portals into its own building rather than large portal rooms (but I also plan to have a central hub when my map gets large enough)