Yeah I read about it and figured that much. So if you're a European, these things are great in Malaccas, Caribbean, Chesapeake Bay, etc. trade nodes. I just dont know how to min/max them. Do you put all the provinces into the trade company, or just the big trade ones, whats good to build, what isnt, and all the other stuff. Ive been playing a lot of blob campaigns for past few months: Mughals, Teutons, etc. but I should probably go back and try to play a tall campaign again just to experiment with more economic mechanics that I am unfamiliar with. I also suck at the diplomatic aspect, for example I never PU'd anyone and have no idea how to.
So there's some tradeoffs involved with them. They use 25% more governing capacity than just a regular territorial core so that's why I'd advise against wholesale TCing of everything you can, especially if you're blobbing.
In general, they'll initially act like territorial cores except for the trade power, which won't have penalties. So a common strategy, taking into account that concern, is TCing the centers of trade in a trade region. Usually, if you get those and/or get them to level two, that's enough to get 51% trade power in a node, which grants you a merchant.
For the TC upgrades, it's important to note that the first two options in each three building chain only affects TC charter provinces (so you have to account for that when deciding whether building one is worthwhile at the time). They are quite powerful such that if, for example, your entire TC charter was set as TC, you would get bonuses almost equivalent to what a fully cored state would look like -- with much less GC. Obviously that costs money, but money is usually more easy to come by than admin mana. The third building in each of the building chains actually affects the whole TC charter (or entire country depending on effect), so you could potentially have stated areas in a TC charter that have 0% autonomy but also benefit from the charter wide bonuses. In general, though, you don't really want to have states in a TC charter because there's more value in using less governing capacity but having most of the value (IF you have bought the appropriate buildings). You can also only have one final building in each charter (so you have to chose one of the five possible). I like the Governor's General Mansion the best in most cases, since it decreases autonomy for the TC charter.
So, maybe to tldr that, TC your CoTs and other high trade power nodes until you get 51% power for the merchant. When you have more money and available GC, build the buildings and TC any of the other developed provinces in that charter to maximize value.
Oh, one thing to note that trade regions and trading company charters are not a 1:1 equivalence. There will often be charters that overlap different trade regions, which can provide for some some complex hijinx.
As for merchants, you really just need to look at the trade flows from other nodes that come into your home node. Keep in mind, you automatically collect in your home trade node, so there's no reason to have a merchant collecting there. When you place a merchant in an upstream trade node, they'll direct the flow to your node based on how much of that node you control. Also importantly, for every upstream node you get a 10% bonus so you can essentially make money out of nothing. You also want to be very careful about manually collecting because doing so removes the trade steering bonus, which can amount to a rather large penalty, so anywhere you collect better be very high value for you based on the trade going through and your control of it (and in that case, a lot of times it would make more sense to just move the home trade node). A situation where having a manual collect might make sense might be if your trade node is somewhere in Eastern Europe but you have a bunch of new world colonies -- almost all of that trade power won't get back to you because it's going to the end nodes in western Europe. So collecting in the Caribbean may actually net you more money in that situation.
At least, that's my basic understanding of things. After groking all of this, I doubled my income in roughly a year after fixing my trade nodes and curating my TC provinces.