Generally mountains are the most random element in your map. While generally they are concentrated in an inland region, there are plenty of examples of mountains near the coast (Rock of Gibraltar for example) or volcanic seamounts jutting up like real mountains.
From your mountains, you can define river, lake, forest structure. Rivers follow natural paths in mountains, so generally if you have detailed mountains you'll have an idea of where the rivers are flowing (valleys, for example, are created by water movement). Lakes occur most often at points where water floods an area, either from a groundwater source, from a river, or from glacier melt. Lowland areas with soft earth tend to see the formation of marshes.
Forests are more random, but water is usually a factor in their growth. Areas with high snowfall will see pine forests growing up and feeding off of snow melt. Mangrove and swamp forests will grow in areas of swamps with thicker earth that allows for them to root. Otherwise forests will grow on the wet side of mountain ranges, along rivers, and in any area with enough water volume to feed their strong thirst.
Towns and cities grow in two ways: they either see natural growth as settlements grow up around water and resource-heavy areas, or see artificial construction. Most major cities in Europe grew along river trade routes, mountain valleys, lakes, coastlines, fertile lowlands, or near precious resources. Artificial cities have grown up in the modern era, sometimes in a fairly natural way (a mining town growing into a metropolis) and sometimes planned (such as Brasilia). It depends on the tech level. After a point you begin to see areas otherwise unsuitable for habitation becoming attractive due to land availability, terraforming, or new resource requirements
TLDR: Generally you start with your landmasses, establish mountains and height levels (I like height projection maps for their detail level), and then figure out water flow based on your region's rainfall patterns. It helps, I've found, to establish areas you want your lakes before making mountains, as it allows you to tweak heights around them. Towns should begin with water-side settlements and decrease in size relative to their positioning.