You can build on any resource that is in your territory.  Once you build a city up next to it, the fence around the city will adjust to go around the resource as well.

You are still getting the benefit from the resource if it's not connected to a city.

Once it's connected to the city, your city will be able to protect it using the units stationed in the city and any city wall bonuses you might have.  Also, if the city has any bonuses to food, your apiary would produce more once connected to the city.

No, he saying it's notlinked to a city.  When you look at a resource, it tells you what city it is "linked" to, meaning what city is getting the resource. and thus, if I want to build irrigation, which city I would need to build it in to get the benefits.  He is saying that when the bee hive popped up, it pooped up in the middle of three cities, and was too far away from any of them and wasn't getting the resources at all.  If they are not linked ot a city, then you dontget the resource even if its in your zone of control and been "built" on. 

Correct.

I hahahaha, I said "pooped up" instead of popped up.  I'm awesome.