Alright, bee keeping.
You need to be in a biome that supports natural beehives, else you can't do any bee keeping at all. No bees in Tundras, Oceans or Glaciers. Not sure about Mountains, since these are now covered with a tiny amount of soil and grass.
First step: Assign ONE bee keeper. Never have more than ONE bee keeper at all times. If you have more than ONE, they will interfere with each other's jobs, like gathering the honey and the jelly from the hive that the other bee keeper wanted to split.
Next: Produce some hives at your Craftsdorf's workshop. Place them somewhere; you only need to know in that regard that they need access to outdoors. If they're on a subterranean tile adjacent to a ramp leading outside, they're fine. You can probably dig a very deep shaft downwards and install the hives in z=0, too, if you want to.
Now, wait that the bee keeper goes to a natural hive, grabs the 12k bees with the help of his beard, and installs them into one of your hives. If you have more natural hives, he will slowly install them into the other hives as well; if you don't have any more natural hives on your map (perhaps because you've walled yourself in), then you will have to wait for a few months until the first hive is ready to be split. In such a case, make sure to "q" over your first hive and to de-select "gather honey from this hive".
During the next 6 months, nothing much will happen except that your cats and dwarves will occasionally get stung by bees. If you like this, place your 1x1 meeting zone right next to the bee hives.
Utilize this time to produce a bunch of jugs at the Craftsdorf's workshop.
After around half a year, the bee hives will be ready to be harvested or to be split. The ONE bee keeper will grab a jug, fill it with the jelly, and place the filled jug and a honeycomb into the "finished goods" stockpile. Why Toady thinks that a hive is destroyed when you gather honey from it, is frankly beyond me. He probably just doesn't know anything about bee keeping.
Then, the bee keeper will -without you having to do any micromanaging to guide him- walk to either a natural hive or a hive that is ready to be split, grab some thousand bees with the help of his beard, and install them.
That's it.
You don't have to micromanage anything, you don't have to de- and reinstall the hives. Just let the little bugger do his job. As long as there is only one bee keeper, he will do this very well.
You then need a screw press to extract the honey from the honeycomb (again, this is definitely not how it's done in real life), and you will end up with a second jug filled with honey, and a glob of wax. Feel free to craft some wax crafts at the craftsdorf now, and sell, cook or turn the honey into mead. Mead should have a higher value than it does now, anyway.