Here's some pics of my setup. All my breeding new species and getting the right traits is done manually, then when a species is finished and 'standardised' they go into the automatic setup.
The autarchic gates on the sides of the apiaries have the 'missing queen or princess' condition so that when the bees are finished everything is extracted out all in one go. They're then fed into apiarist pipes, with princesses going up through the white route, drones going down through black and items heading right through the blue route. I've got four of this setup chained together with all the items exiting the right side into the processing area. The first drone is fed back into the apiary with the 'drones' condition, further ones exit into the void pipe with the 'any bees' one. The void pipe can be replaced with a chest if I need drones but at this point I have quite enough so all excess drones are getting voided.
In the processing area combs are fed into the hopper on the centrifuge, with a 'has work' gate to turn on the peat engine when needed. The fact that all combs are extracted at the end of a queen's cycle rather than as they are produced helps with not wasting fuel. This works especially well if you have identical princesses which are synchronised together like my two tropical princesses, who offload 5 or 6 silky combs each at about the same time.
Another autarchic gate and wooden pipe empties the centrifuge, and loops honey drops and silky propolis back into the original item line. Other items head into the gold chest. The silky propolis goes back into the centrifuge with the combs, and the honey drops carry on into a squeezer with a similar 'has work' gate setup to the centrifuge. The honey is then piped into the iron tank which in turn keeps the analyzer full. A final autarchic gate pumps the propolis into the bee products chest.
I usually wait for a buildup of honey drops before I put peat in the squeezer's engine as I sometimes want to save a stack for other things, and it's more fuel efficient to squeeze a lot at once anyway. Bees is the thing I do a lot of manual work on while all my other automatic stuff slaves away so I'm usually around to keep an eye on it.
At the minute I've got the two nocturnal, poison free, normal biome tolerant tropical princesses I mentioned going so I plan to add a carpenter that makes woven silk automatically when I enable it, and later swap it over to make candles. The other two princesses are fast Industrious, I'm using a third to try breed a nocturnal version at the minute. I have Majestic going in my manual apiaries but haven't standardised an Imperial princess yet. Once I've done that and got royal jelly it's on to getting an alveary for my demonic princess so I can get her out of the nether for good, hooray!