How do you subdue the bees?

Go to apiary. Make a smoker based on the bee book. In inventory, click tobacco pouch on gear to disassemble it to empty pouch and tobacco.
Combine hurricane lamp and tobacco to get lamp with tobacco.
Combine lamp with tobacco with garden hose to get unlit smoker.
Combine unlit smoker and matches to get makeshift smoker.
Use makeshift smoker on a beehive. Open beehive when they are now asleep.
Take a honeycomb frame.
Combine honeycomb frame with cocktail shaker to get cocktail shaker filled with honey.
Combine cocktail shaker with a glass to get a glass with honey.

*Go to the study desk and use desk key on left drawer. Take the bee book and enter it on the journal. Read the journal to learn how to make a smoker-please also note you need a key to open the draw,you can get that if you look around the games room (on top of the cabinet by the pool table *hint*)

Hope it helped!