so I set a merchant to collect there and immediately started earning another 4.2 ducats. I'm not collecting in Sevilla, just steering to it.
So you already moved your trade capital is what you say?
If so, you should try sending your merchant to another location than genoa itself and see, what that does with your income. A merchant in your home node does only give you 2 Trade Power, which is ridiculous.
It seems like you are not very familiar with all the rules EU4 has hidden in it, so i would not suggest to try some "pro strategies", restarting early etc.
Instead, play this game as long as you have fun with it and try to learn as much as possible. The game changes quiet drastically in the late game, and you need as much experience as possible to get a grab on the whole colo/trade/war system.
Ottomans were always really strong, IMHO they only became even stronger with the last patches, so it is probably somewhat harder to learn how to defeat them today than it was when most of us started playing.
Regarding Portugal: As long as they are colonizing, i would not integrate them but let him do his job. They are and always will be catholic and in the same culture group like you, so every province they will give you will be as valuable to you as if you colonized it yourself.
You might want to activate the subject interaction "divert trade", so they give you trade influence, which is very important for ivory coast and especially Seville.
Check their liberty desire first, though, since this will increase it by 30%, and as soon as they become disloyal you could get problems.
If you don't want to hassle with portugal anymore, because they annoy you by colonizing where you want to have the land yourself, LD gets critical, etc., you can still integrate them with no big loss. You might want to have Influence Ideas perk 3 first, though, since they might be quiet expensive to integrate by then.