As far as plate tectonics are concerned, I have found that pretty much any mountains, cliffs, and topography can be explained some way or another; however, climates are very hard to explain without magic. That is why I find that I place coastlines, mountains, and a couple places I know I want (such as a city in a forest here, a desert there). Then I can place winds and rivers to help make it seem both realistic and look like how I want it. My tip for you would be to place mountains, and then look at my giant post about climate and winds for reference on how to place climates.
If you get stuck placing mountains, I often print out a copy and pencil them in so I can get a feel for what I want before I go back to the computer.
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