The most common way to micro manage is to manually lock every single citizen however you want and then set to production focus, so that new citizens grow to production tiles. We do this because when the turn rolls over, if the citizen grows to a tile with lots of food, the food doesn't register for the next turn's collected yields. However, production does do this.
As to what tiles to lock, it depends on what you're working towards. 99/100 times that'll be quick growth balanced with tolerable production, but sometimes if you think you don't need your city to keep growing, or if you're wanting to work hammers or science or gold, or a million other reasons, it's worth it to not work the growth. But I mean what to selectively work isn't as important as locking the tiles you do want to work. Every time you get a new citizen in any city, lock it on whatever tile you'd like to work, and keep the city on production focus. It ends up knocking many turns off of your production every game, meaningful turns that can mean the difference between winning and losing.
Specialist wise, work every scientist specialist you can afford to work in every city all the time. If the city stagnates or starves don't do it, but it's okay to unwork a mine for scientists, as long as the city keeps growing. If you run out of tiles to work and scientists to work, start working engineers unless you've got a guild in the city, in which case work the guild. In fact, guild specialists are the only other kind of specialists it's okay to unwork mines for. So the order of things to work, for the most part at least, would be:
-Growth (including cow and sheep pastures, hill farms, etc; 2-growth tiles count if they have good hammers)
-(Natural wonder- rare)
-Scientists
-Guilds
-Reasonable hammer tiles (mines, horse pastures; 1-growth tiles count with good hammers)
-Engineers
-NEVER merchants
You can work GOLD TILES if you're low on gold, like plantations etc. However do not work merchant slots unless you've got secularism AND Statue of Liberty AND the freedom policy of food on specialists.
And academies work in your capital whenever you've got proper growth still, although normally your academies should go on food heavy tiles already. I normally build them on tiles that already have a 3 food 1 hammer yield, like stable cattle and granary plains wheat. Normally avoid academies in river tiles and hills, unless you have to.