If you use the mousepad/sandpaper method you will create a convex edge.
I know this may sound a bit confusing, but you can create a convex micro bevel. A "full" convex follows the same curvature from the spine all the way to the edge. Like the shape of a bullet.
A "convex micro bevel" is formed when you change the angle right near the edge and create a micro bevel, with rounded edges.
It is hard to describe, so here is a link with some good diagrams and explanations of full convex and micro convex.
http://www.kosterknives.com/convexedge.htm
In reality if you freehand sharpen with a stone, you will still likely end up with a micro bevel that is convexed to some degree. This is because you can't hold your knife and stone at perfect angles as you move the blade along the stone. This "wiggle" action will create a rounded corner on the bevel.
If you want to maintain a true "flat" micro bevel you need to use some type of jig that will hold the knife edge and sharpening stone at a steady angle.
Hope the link helps explain it.
Kevin