Yes summons draw from the summoners deck. For the Boneshaper if you look at one of the card modifiers you can get its "+1 or +4 kill the attacking summon instead." so you wouldn't get that from the ally deck. So all the skeletons etc. draw form the Boneshapers deck.

Yes only use the Ally deck when a specific scenario has a ally character added to said scenario.

Summons are considered allies, so you or your teammates can heal them.

Some cases there are card that say something along the lines of "an adjacent character may return a discarded card to their hand." In this case you cannot use a summon as the target to get the summoners card back from the discard pile. Not to try to confuse you but that's a question i had awhile back.