I think the new system is great, but it's definitely overwhelming at first. My advice is this:
At first, build very few specialist buildings. Go for mining / agri / energy districts. When you do start building specialist buildings, keep these two impacts in mind:
1. The job will take worker jobs away as they get promoted to the specialist job (so now you're getting fewer raw materials until those workers are replaced). This will be recovered over time, or immediately if you have unemployment on that planet.
2. It will also take away resources. Minerals go into allows and consumer goods, and labs will take consumer goods (which in turn came from minerals).
This means you need to think long and hard before building specialist buildings, and you want to ensure a strong production of raw resources before going up the tech tree. Secondly, only build one specialist building at a time, and wait for the population to regrow.
This means you want to be comfortable with that little orange house next to your planet indicating that you have a building slot free. Only build when you know you can afford it (building production districts, on the other hand, will have no negative impacts on you whatsoever).
Be even more careful about upgrading specialist buildings. After the first stage they start requiring gas, crystals or motes. This is where the interface could be improved - you have to hover over the strategic resources to see how much you are producing. Maybe that information could be shown whenever you're thinking about building / upgrading something which requires that resource?
I think it would also be nice if, when hovering over a specialist building, you get detailed information about how many resources go in (per job or even for the whole building if all jobs are filled) and how many go out, similar to what the population tab shows, to make planning easier.