Ok so its not usually a problem to have mesh that intersects or overlaps slightly.  I was trying to delete clothing covered body mesh then weld the verts of the edges of those holes onto the edges of the clothing mesh to close those holes... 

So for instance if I have a shin going into a boot... I could delete the foot and cap it as well as capping the boot then just have the stump intersect into the boot geometry slightly.. rather than trying to join up the stump and boot geometry into one object.