For standard layout the lift from the stab (whether it's positive or negative) is negligible as far as wing loading is concerned *)
The difference in incidence of the stab and wings is called decalage. For longtitudal stability you want to wing to stall before the stab.
What are the benefits or disadvantages of a flat bottom airfoil? Very difficult to answer in general terms, without discussing some specific airfoil. For me the biggest advantage of a flat-bottom airfoil is that the wing tends to be easier to build. Symmetrical airfoils are good for inverted flying
*) not entirely true, in some rubber powered classes with wingspan limits the contestants tended to use larger than scale lifting stabs to increase total lift