Hello, I've been playing the beta for a very long time and have beeb figuring out a few things for those who have played the game for some hours and are looking to improve even more. I deliberately put the "pro" in quotation marks because I am sure that I have not (yet) mastered the game to perfection.
This is not a complete guide, there will certainly be other and better ones. I'll add a tip every now and then when I discovery something new and I'll have some screenshots to show what I'm trying to describe. I no longer have access to the beta, so I couldn't take any new pictures yet.
Please note that I wrote the original guide in German, so this English version might be a bit clumsy at times, but feel free to correct me.

First things first, because pretty much everyone has played the old classics: Yes, we have an isometric 2D city builder game here, but it is not a pharaoh clone, instead Nebuchadnezzar sets its own accents, which can be found primarily in the field of logistics: Range, addition of workforce, utilization and layouting of available space, etc.
Please always keep this in mind whenever anything seems unexpected to you.

All farms can cultivate 18 fields per worker slot (in the following, for the sake of simplicity, I will use the term workers). I recommend creating 18 fields per worker and leaving free fields <18 to a second farm and not filling them up with another worker.
The reason for this is that a worker with 18 fields receives a yield of 9 goods per harvest. These are optimally used by two workers in processing factories (4.5 goods per year and worker are converted into end products). With 3 farmers of 18 fields each, this results in a yield of 27 goods of grain (as an example), which are baked by 6 bakers into 27 breads. 6 bakers can work in exactly two bakeries. It couldn't be any better.
By the way, more than 3 farmers per farm is not possible in a perfect way. 4 farmers would need 72 fields. A farm including its range is 9x9 tiles in size, requires 9 tiles for itself, so that 72 remain. Unfortunately, you then need a road that leads out of the farm.
For farms such as milk production you can of course fill in the remaining fields with another worker. But I prefer to keep products from one housing category at the same level, an exception would be the additional export of milk, e.g.

Sounds strange, but it is like this: Single (simple) houses each consume one good per year. That doesn't increase when the house is upgraded and new immigrants have arrived. New products are surely expected, but the old goods are consumed as before.

Use the statistics regularly to keep an eye on the consumption of your citizens (plus exports) and to compare that with production (plus imports) in order to recognize early when you are producing not enough in specific category.
You'll see the annual production and consumption of every good. If you produce more grain (e.g.) than is "consumed" by making bread, you have an unnecessary surplus of grain doing you no good. In the opposite case, not as much bread is baked as it would be possible.
It is also important to know that houses store up to a two-year stock inside or rather receive up to that amount from the market staff. Therefore you have to produce a little more than is consumed by your citizens. If the consumption corresponds exactly to the production, maybe not all houses will be supplied fully at the same time.

The game lives from range and fast transport. For dairy farms this means: a warehouse should be accessible from the farm's transporter, ideally as close as possible so that the transporter can complete his task quickly enough. Otherwise the internal warehouse of the farm will fill up and no more goods everything can be harvested, or another transporter has to be hired which takes away valuable global workforce.
With a grain farm things are a little different: Here bakeries should be close to the farm (not necessarily a warehouse) and these bakeries themselves should be close to a warehouse to deliver the bread. In this example, the grain does not have to be temporarily stored.
Milk and bread should in turn be in the immediate vicinity of a market and the market, in the best case, close to the houses to be supplied.

The screenshot shows this interaction here.
Let's start with the "red way": The grain farm's hauler delivers the grain to the bakeries as well as the bakeries' transporters can get the goods from the farm as well (step 1). Once the bread is produced, these haulers store them in the warehouse (step 2), where a market employee gets them (step 3) to provide them for the market ladies for further distribution.
Theoretically the market's transporters could fetch the breads directly from the bakeries as well. But achieving that fast enough is mostly too much to ask for.
Continueing with the "yellow way": Starting from the farm the milk is brought to the warehouse (step 1) and afterwards taken from a market hauler for the provision of the populace (step 2).

In contrast to the earlier games, storage yards do not have their own transporters. They are basically just an area in which any goods can be placed and removed again. They do not use any workforce, and therefore they cannot collect or distribute goods independently.
Positive side effect: all 9 slots can be equipped with goods, so the space with 36 goods is slightly higher than with Pharaoh and co.

A very interesting point is the following: clay pits take up a lot of space, cannot be built everywhere, but are needed in large quantities (for pottery, bricks and other items). If you now have processing factories within reach, their transporters are totally sufficient to collect the clay. The transporter of the clay pit can be dismissed and replaced by another worker for the clay extraction.

Fellow player Panacea has made some interesting observations I like to share with you:

• Your farms have an own storage of 20 items - per crop you plant. That means when you sow more than one crop, your storage multiplies. Only grain means a storage of 20, the combination of grain and dates provides you with a storage of 40 (20 for grain, 20 for dates).
  
• A caravanserai does not care if an item is locked in a storage yard or not. It just takes or delievers the good it is supposed to. That is quite a change from the early days of this game where the storage yard decided which resource was to be delivered or taken from. Now caravanserais have all the power and even override the storage yard's instructions.
  Maybe you can think of some cases to take use of that mechanic.

Thank you so much, Panacea!