Problem with modeling
 

almost every time I try to model somthing I somehow mess it up so I get a nonmanifold geometry and I don´t know how to fix it. I know I can go to polygons - cleanup but that seams to split the vertexes so if I try to change the model to a subdiv it gets all messt up whith holes and stuff. But if I merge the vertexes back together I get the nonmanifold geometry again. It´s like a vicious circle
What can I do to fix it?