I have seen many old and big players doing the same mistake too...It doesn't matter to them because they have enough money to cover the losses. But it is a big thing for the new players.
Here in this guide, I will hopefully help you in chosing which area you should build your buildings in.
Production Buildings:
Here are some production costs of products in the three areas:

*The ratio is the decrease in production cost from the earlier area.
If you noticed:
Production cost decreases by 1.666... times from red area to the yellow area
Production cost decreases by 2 times from yellow area to the green area.
This is true for ALL PRODUCTS in kapilands(except for extremely cheap products like power becuase its difficult to find a number exactly in the same ratio)
Now, to calculate average profits we will need three whole numbers that fall in the same ratio:

Let's say there is a products that uses these production costs and you can produce 1000 of it in 24 hours/1 day.

CLEARLY,
Green area gives the maximum DAILY profit...And red area gives the LOWEST.
For new players, the 25% extra production sounds a lot. But it really is giving you lower profits while you could earn higher profits by buying a cheaper building!
Now, for wells and mines.

NO DOUBT! Wells and mines should never be built anywhere except the yellow area. As you can see, the yellow area gives you around twice as much profits as the red area! That is a truly a lot.
Farming and Plantation products produce 25% faster in the green areas. Extra production in an area with the highest profits! You don't need a spreadsheet to tell you where to build farming/plantation buildings.
Research Centres:
These buildings should be built in the red area. As you go on researching, the research time increases highly exponentially. 20% faster researches could save you days of research. And you could use those saved days to produce high quality products which you could sell for higher prices! If you are a new player, you may build a research centre in the green area to save some money, but faster research will earn you more money than saving you any.
Stores/Shops:
There are no specific areas to build these in. YOu should normally go to "STATS" and check out which country sells your product for the highest price. This countries are mostly in the red area. You might not mind selling products for lower prices to save money, but if you notice: Red areas sell products for nearly twice the prices of other areas. I don't know whether only red area has the highest selling prices, but you should always see which country WITHIN the red area sells it for high prices.
SUMMARY:
All production buildings except wells and mines in GREEN AREA.
Wells and Mines is YELLOW AREA.
Research Centres in RED AREA.
Stores and Shops in RED AREA but in the RIGHT COUNTRY with the HIGHEST SELLING PRICES.
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I hope this guide help a lot of new players and probably changed the way older players think.
If any for you notice a flaw in my calculations OR notice that I haven't taken a specific factor into view, please tell me so that I can recalculate and edit this post to help new players get accurate calculations.
Thank you!