Yeah, when you look down in blender (numpad 7) it should be what you're used to--positive x to the right, positive y up, positive z towards you.  Unfortunately, this maps to looking from the front (numpad 1 in blender) in most other applications.  Just model what you would do from the front view in another application from the top in blender and it should be ok in another application without rotating.  I model almost everything like that because it's just easier to think about.