Well, there are a lot of ways to approach this but this is what I do. I make my world as geologically accurate as possible as if mother earth made it herself...but within reason. I'm not a fanatic zealot about getting my continental plate boundaries and climate patterns all that accurate..."good enough" is good enough. Then I go back and fit in whatever elements need to be in certain places...like a swamp here, some mountains there, etc. If this doesn't fit with the underlying terrain then I have to alter the underlying terrain a bit to sort of "blend" things together...like a desert right in the middle of the continent isn't all that natural unless mountains and climate permit it. If those elements aren't present I either add them or tweak what's there to make it work, like having no lakes or rivers.