2nd wave colonizer/trade companies strategies?

Hello. I've been playing as Florence -> Tuscany and I decided to take Exploration as my 3rd group (Innovative, Plutocratic, Exploration). Unfortunately, I'm having a relatively hard time getting anything done. So here is my question, is there any tips you can give me about that? Anything, literally.

And here is how my situation looked like. You can skip this part, it's mostly a lot of details that might help in giving tips, but thank you if you decide to read through:

I constantly had a ton of income, lvl 2-3 advisors and still getting 10 ducats a month or so. What was my plan, I picked the repression and killed the natives obviously as I couldn't afford to keep my troops in my colonies, I had to keep fighting wars in Italy. I wonder if native coexistance would be a better choice? Anyway.

Americas. When I joined colonization (tech 10) my range was really short, I barerly reached Guinea so I had no way of getting some colonial nations. Also, Brazil was already claimed by Spain, Carribean soon after by Portugal. If only I could I'd get some center of trade, unfortunately non were available, so I colonized some islands just for the sake of a naval base, while obviously angering Pope for breaking Treaty of Toredesillas. But, the important thing is, I didn't see a reason to colonize further. Columbia was soon after claimed by England (altrough they became anglican later on, so I colonized Panama region), I have no way of steering trade from northern america, I have no way of fighting Portugal (that blobbed into Marocco really hard), I had half of their navy + they were allied to Spain (my ally too) and GB, no way of fighting Spain obviously, so I abondoned the idea of colonizing Americas.

Africa. I didn't want to leave a single province by itself, so I colonized entire Guinea region and then Gulf of Guinea while killing natives. At first I kept them as full states, like 100 years after that I changed them into trade companies as I lack any more governing capacity. Then I tried to go for South Africa, but it was already taken by Portugal, so I colonized Natal region with a plan to then start fabricating on Mutapa and Kilwa, but they had armies equal to mine, I couldn't afford to send all I had down there in case any of my allies calls me into a war. Then I hoped to colonize some islands on Indian Ocean, but here came my problem, I have no way of benefiting of that trade. I will get a couple of % in Malacca or India and what? I can't steer it to Genoa or collect as I don't have that many merchants for that.

Also, northern africa. I think Tunis is rich enough to keep it as full state, right? Sure, I'm having a problem converting them for now, but in the end I will get the majority of trade and by simply accepting or culture converting I have quite a bit of manpower and taxes too. But I really don't know, I didn't even think I can make a trade company of something so close.

And this is my final point (probably), trade companies. Maybe I'm wrong, but in the end I feel like they bring you more than full states. If I didn't kill the natives and kept that shit ton of production (and trade) it would be much more profitable than tax and manpower. Anyone can confirm that?

So here I am. Late for Americas and Africa with no reason to colonize further the east. As I said, my plan now is to try out native coexistance policy, maybe take exploration as 2nd idea (from what I just checked, on tech 7 with the +50% range and an advisor for +20% range I can barerly reach Guinea region from Pisa).

I think that was needlessly long, but I didn't want to miss any details in case that helps. Thanks once more for reading and thanks in advance for any tips!