Is there a list somewhere that says which side quests go with which Hero and Monster collection? Or are they all mixed up? The Collection Manager in the app itself had no detailed information to offer about this.

Yes, it does say:

-Bonds of the Wild: Choose your poision

-Crown of Destiny: Time trials

-Crusade of the Forgotten: Gather no moss

-Guardians of Deephall: Stand at Thaurgrim's Rest

-Oath of the Outcast: Bound by fear

-Shards of Everdark: Let them go

-Stewards of the Secret: Tooth and blade

-Treaty of Champions: Prisioner of icespire

-Vision of Dawn: What bring us together