Lake Silencio is on top of/nearby the underground bunker in Utah from Season 1's 'Dalek'.
Because the Bad Wolf retro-ripple would be a handy explanation for why that part of Utah is primed for a fixed point in time.
The Silence offed Madame Kovarian for failing, not uselessness.
This was the Kovarian faction's second (or first) big scheme to get rid of the Doctor so he can't reach Trenzalore and potentially start a second Time War...and failed so miserably they almost destroyed all time and space. Rather than simply being cold-hearted, the Silence realized Kovarian was a liability more than anything and disposed of her. If you interpret the "use River as an assassin" as Plan A and "blow up the TARDIS" as Plan B, it's the Silence deciding they should just be in charge of the plan themselves...which went even worse. The reason why Kovarian and the Silence never went after an earlier incarnation/only show up in the 11th Doctor's time is because they realized all they were doing was making things worse.