First, how exactly do I know when to use the monsters that have been "set-aside" for Shub? I'm assuming I use the Dark Young and Goat Spawns to spawn on Cultists during reckoning, but how about the Ghouls? I don't see what mechanism allows them to enter the board. And when the Dark Young and Goat Spawns are killed by investigators, do they go to the cup or do they get "set aside" again?

Lastly, every reckoning I also spawn an additional random monster thanks to Shub and advance the Doom counter by 2 if there are already 10 or more monsters on the board. Doesn't this mean with some mythos cards the doom track might advance 3 or even 4 spaces in a turn (due to omen and gates + reckoning) ?

One of the mysteries spawns an Epic Monster that brings ghouls onto the board every time there is a reckoning.

We've played it that you set aside the Dark Young and Goat Spawn monsters when you defeat them. (Basically to make it easier so you don't have to continually search the monster cup when you have to replace the cultists.)

Yes, some Mythos phases could end up with a lot of doom track advancement. To be fair, if you're not keeping the number of gates under control you can get a lot of doom advancement even without having 10+ monsters on the board. Keep the monster level down and close those gates!

Shub requires a lot of monster whacking. Don't be afraid of multiple doom advance / round: IIRC, in one game played against Yig, I got a +7 doom in one single round (needless to say what the final outcome was)

As for monsters: they enter play also through "monster ambushes" triggered by Research Encounters.

Setting aside monsters can be tedious, but also helpful in some cases. Killing a set-aside monster results in the monster to be returned to the AO sheet.

You have a detailed explanation of "set aside" in the Reference Guide, pag. 10, under "Set Aside"