The two moles are because you added enough strong acid (HCl), 2 molar to be exact, to convert all of the base to conjugate acid. Therefore, your starting concentration of conjugate acid is 2 molar.
[HSCH3] <-> [H+]*[SCH3-] with a pka of 14-3.6= 10.4
So,
10^-10.4=x^2/[2M]
As for your second question, that equation is only valid when dealing with a weak base or a weak acid in equilibrium at a certain temperature. As you should know, strong acids and strong bases dissociate completely in aqueous solution.
EDIT- actually, I believe that it is not 2 molar, I beleive it is one molar. Because when you add a 2 molar equivalent to another 2 molar equivalent, you have 2Moles/liter +2 moles/liter of something else. The moles combined [H+] + [SCH3-] to get 2 mole of
[SCH3-] Meanwhile, you are also combining 1 liter+ 1 liter which will give you two liters of solution. Therefore your total concentration should be 1 molar solution giving you the equation,
10^-10.4=x^2/[1M]
Which would indeed add up to the answer you provided.