I’ve found that the easiest way to make sure my maps don’t end up looking wonky is to start with watersheds or drainage basins. Which sounds about as sexy as long division, but bear with me.
A drainage basin, roughly defined, is an area of land where all the water in that area drains into a particular river. Since I’m an American, I’ll use an American example: pretty much the entire region between the Appalachian Mountains and the Rockies is the Mississippi River Basin. If you track the big rivers, they flow into the Mississippi. If you track the smaller rivers, they flow into the big rivers that flow into the Mississippi. If you — okay, you get the idea. Rivers that don’t flow ultimately into the Mississippi probably either flow into the sea or other large body of water (like one of the Great Lakes), or else they go underground and from there drain into the Mississippi. (Or not. I think they can do weird things once they’re underground. But since they’re underground and therefore not on most maps, I don’t much care.)
“Watershed” can mean a basin; it can also mean the dividing line between basins. The Rocky Mountains are a watershed, separating the Missisippi Basin from whatever the one to the west is called. We use this as a term for an important moment because it changes the direction of things; one minute they’re flowing this way, the next minute, some other way.
So if we imagine that you’re drawing what I think of as a “complete map,” i.e. something bounded on all sides by water, then one thing you can do to make it look coherent and natural is to draw in a couple of big rivers running down to the coast, slap some mountain ranges down between those rivers, and then work from there. This principle also works with smaller units, but I find it’s the most relevant when you’re dealing with large areas of land.