Welcome to WAMAS.
1) 2nd hole may not be a drain at all. This actually may be the return pipe.
2) Maybe they took the liberty of shaking off loose particles for you, hard to say sometimes.
3) You can turn them all on at the same time, but most of the time folks just turn on the skimmer until the tank has cycled.
4) Yes, you want to grow bacteria, but turning the equipment on, won't kill all of it.
5) You can leave the lights off, some folks start/program their normals lighting cycle, others just leave things off until they notice dinoflagelattes.
6) Not sure, but I don't think so.
7) You don't need to add algae to the tank yet, but you could.
8) When the tank hits the dino algae stage, give it some more time, but you could probably add clean up crew members (snails, hermits)
9) Pinch of food could help with the cycle (allows the bacteria to grow off the decaying food)
10) Just one shrimp will be fine.
11) Just add the shrimp, won't be as messy, but you could do both.
12) You don't have to monitor Phosphate just yet. Keep track of PH, ammonia, salinity, nitrate, nitrite. What you're striving for is the initial increase of nitrates and the overall decrease of nitrites and ammonia.
13) You don't have to do a water change until after the initial dino algae, but if you wanted to, you could.