How are the two ATPs (properly 1.5 though) formed from oxidation of 1 FADH2?
FADH2 substrate does increase the H+ gradient by 6, and so increases the ATP Synthesization "potential" by about 1.5 (6/3.3). the difference between the NADH and the FADH2 substrats are mainly the different path in the electron chain. NADH uses Complex1, and FADH2 is part of Complex2, which have different ability to to pump H+ out. (but of course there are many other differences).

About the second question, it's a really broad subject involving the Krebs cycle and Glycolysis among other subjects. it is mainly a matter of enzyme regulation. The regulation affect both the electron chain and the ATP synthase.