I normally use default unwrap and then sort the UV Map according to what I want.  Using material groups you can also use a sort of "hybrid" method using default for some parts, cylindrical for other parts (there are certain cases where this is really useful).  Smart unwrap is its own thing however and while it makes very efficient use of map space is virtually unusable in a 2D paint application (it generally breaks the mesh up into a lot of small blocks and arranges them in the most space efficient manner, which generally makes it very difficult to paint on in a 2D app later).  I normally use smart unwrap on a hi-res sculpt where I paint directly onto the object mesh within Blender; and use other unwrap methods for my final model.

On the Bleed setting, I find that a setting of 8 generally gives me good results.  However, if I still get a visibile seam I may open the texture map and paint directly on it within blender.  I'll use the eyedropper to get a sampled average color of whatever texture I'm stenciling and then use a brush to feather that in around the edges of the islands.

Another thing you may want to try is doing a split window (or if you have dual monitors, open a second instance of Blender on the 2nd monitor) so that you can watch the UV Map while you paint to see how your stencil is being applied.  Sometimes that gives me clues as to what might be wrong (maybe I need to adjust my seam or move the islands on my UV Map, etc.).  You can even use the stencil directly on the UV Map in some cases to touch up a problem area.

BTW, if you don't have a 2nd monitor but do have a HDMI 720i or 1080i TV, you can get an HDMI cable and use your TV as a second monitor (which is what I'm doing).