to get to the underground jungle you go under the jungle and keep going until you reach cave level

to find the queen bee you need to go to the underground jungle and once your there you look for a hive that is colored yellow then you go into the hive and look for a larva it looks like a bee in a giant yellow oval thingie

to kill the queen bee you will need some armor and a weapon of some sort (of course)
when you go in the hive and find the larva attack it and it will break once it breaks a message saying the queen bee has awoken will pop up on your screen then wait for the bee to come and kill it from there