How does hot water get circulated into an indirect fired hot water heater?
It's because inside the tank there's a coil in which circulates hot water from boiler (without mixing with clean DHW). The boiler is connected in a 'closed loop'.

The 'loop' connections are on DE, clean water enters at F and hot water exits from B.

I think they call both 'outlet' because you could use the lower one also as outlet when you drain your system. Also input to boiler sounds little weird to me.

Another option is if that thank is used as 'cold' puffer for AC: heat pump cools water inside then water is 'recirculated' trough the fan-coils. In this case return from fan-coils should be plumbed on B and cold output to F

top to bottom:
1> hot water outlet  (B)
2> input FROM boiler (D)
3> output TO boiler  (E)
4> clod water inlet  (F)  

also check this