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.