I've been playing a bit of Napoleon TW lately, and notice a little bit of a lack of information from the non-battle side of things. The army battles have the most impact in the actual campaign, but it is buildings and towns that allow you to build and reinforce (and upgrade) your armies. Therefore; knowing what buildings to use is very important. For this article, I will be using "town" to refer to the small; non-unit recruiting areas in a province that buildings can be built on and "city" to refer to the larger "capital" areas that are used to recruit units and capture the province.
Napoleon TW has introduced a change from Empire TW in that towns now come in three flavors. Instead of being able to build a manufactory, church, school, or entertainment building; you are given a choice of two buildings per town, and towns are classified as Intellectual, industry, or commercial (which determines which two buildings you have access to). This is in addition to the usual province improvements like ports, logging camps, mines, farms etc. Cities function similarly to those in Empire TW, but there are some changes. As towns have the largest changes, we will look at those first:
Intellectual Centers: These allow building of Colleges and Members Clubs. Colleges function much like the schools of Empire Total War; and research technology and spawn gentlement. Members Clubs are essentially the entertainment buildings of Napoleon; raising happiness and spawning spies. When choosing between these two buildings; you must balance the need for happiness with the need for technology. Also remember that technology buildings increase clamor for reform in the province they are in, which means a province with a low happiness would be better served by a Members Club.
Industrial Centers: These allow building of Manufacturies or Gunsmiths. Manufacturies act much like they do in Empire TW; adding a sum to the province's wealth, but also provide a reduction in cost to artillery recruitment in the territory they are built in (and given the power of Napoleonic Artillery, this is not a small bonus). The gunsmith reduces the cost of infantry by about the same amount as artillery cost is reduced by the Manufactury. It should be noted that while the manufactury seems like a no-brainer to build over the gunsmith; infantry is going to be recruited more often than artillery (as it is more likely to be destroyed and more common in armies). A gunsmith in a recruiting center can be worth many times more than a manufactury, even when the taxes are brought into play. Always remember that both of these buildings spread unhappiness among the lower classes.
Commercial Centers: These allow the building of Supply Posts and Markets. Supply posts are some of the most important buildings in the game; as they replenish your damaged units at a higher rate than the base province level. Markets, on the other hand, improve province wealth and wealth per turn. Depending on the speed of your advance, the usual strategy is to build supply posts in advance territories along your path of conquest, and replace them with markets as the front moves forward. Alternatively, you can ignore supply posts altogether, and rely on the natural replenishment rate (which in connected provinces that have sufficient building capacities is decent). Personally, I still build supply posts in the front lines, unless the battle is moving forward swiftly. I rarely build a lot of supply posts at once.
Now to discuss changes in the minor province buildings. These changes impact the mechanics of Napoleon Total War, and should be considered when deciding where to spend your gold:
Farms: Farms increase the replenishment rate of units in the province, as well as adding to the wealth of the province.
Stables: Reduce cost of cavalry units recruited in the province and increases province wealth.
Logging Camps: Reduces the cost of buildings in the province it is built in by 10/12/15% (very nice bonuses, and this is a building you should upgrade first). Also adds to province wealth, and reduces the cost of naval unit recruitment in the province.
Gold Mines: Adds to region wealth and also increases region wealth per turn.
Iron Mines: Adds to region wealth, but also reduces the cost of unit recruitment in the province it is built in.
Cities: Cities operate very similarly to Empire TW. They have a town center as well as several other building slots depending on their size. They can usually build walls as well. The extra slots can be used to build an infantry/cavalry recruitment building; an artillery recruitment building, and an entertainment building. I believe the admiralty returns as well, but as I rarely focus on the navy I am not 100% sure on that. These buildings function very similary to those in Empire TW; so look at their information scrolls for specific information.
That should give you a basic understanding of the bonuses involved in these buildings and should help you decide what is and is not worth building. Personally, I focus one or two provinces on recruitment (giving them the recruitment cost reduction buildings and building up their cities to build all kinds of units) and the rest on economics (building Manufacturies, markets, and the like). Your mileage may vary.