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Each ATP Synthase has three sites for binding three sets of ADP and Pi, so when the H+ pass through the a and c subunits are they (3 ATPs) not produced for FADH2 substrate?

Besides is the respiratory chain linked to the phosphorylation process apart from the trasfer of H+ ? How does the cell know which substrate has been oxidised and how much ATP is to be produced?

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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.

Electron transport chain

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