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I like to maximize the value of the particular manufactory:
Brewery in sugar or wine producing province
Naval factory in fish or naval produce
Art Academy in Capital province

If you have a grain province a brewery still gives .5 montly income.
So I would look what the CoT province produces to determine what you might want to build in that province.

Manufactories in provinces reporting to the CoT also enhance the value of the CoT itself, as well as tech bonuses.
 
Where to place manufactories?

This is what I'll do......

Step 1 - decide what kind of manufactory you really want.

Each manufactory contributes to one specific technology area. So that depends on which technology is more important to you. Normally, naval tech is almost always less important than land technology, and infrastructure tech is almost always less important than trade technology, and your stability should almost always be +3. Therefore, you should focus on weapon manufactories, and refinaries.

Step 2 - decide where to build it.

Criteria for choosing (in order or importance):

a. should provide the max bonus. For a refinary, it should be built in a province with wine or sugar. For weapon manufactories, it should be built in a province with copper or iron.

b. should be built in a province where you do not expect to be attacked. Manufactories are easily destroyed in wars and sieges. A good example is Opporto. It has wine, but it is a favourite target of the AI nations, especially England and other northern European nations.

c. should be built in a province with minimal revolt risk. The reason is same as (b). There should be no nationalism left, and the religion should be the state religion, or a religion that you are very tolerant of.

d. should be built in a province where you want a higher population growth rate (such as a colony in India). Manufactories help with population growth rates.

This is what I'll do, not necessarily the best way though.
 
Naval Manufactories

Just an addendum in a specific case (England in GC):

I build a naval goods factory in Bristol, since England gets no shipyard without conquest. It's a long wait until Naval Tech 16! England also has no wine/sugar until colonization.