Some thoughts on colonization, all from my IGC experience, your mileage may vary --
(1) If you plan to do lots of colonization, especially by seeding (getting a colony up to a decent size and then just letting it grow to city size on its own) than keep in mind that the growth rate listed in-game is actually more like % growth per decade rather than per year. I don't know whether it still works this way but some island provs with big growth rates may actually break that rule and grow much faster (Port Royale gets mentioned for this a lot).
(2) Keep in mind that colonists can also be missionaries. So long as the province isn't over 5000 population, sending your colonist there will change the provincial religion to whatever your state religion is. This can be very useful!
(3) Possibly because of rounding, but I've had colonies with zero pop growth that do not advance as normal at 600+natives/700 colonists. That required sending an extra colonist -- happens in the very inhospitable areas like India or Africa, especially if you also have a neighboring COT (at stability 3, -2% growth is very common there, which is exactly offset by the +2% bonus for a neighboring COT). Speaking of which, in such negative growth areas, you will have to send additional colonists anyway to offset the population losses.
(4) Natives -- even low and very low aggression ones -- will often attack when an army first shows up. What you might want to do is figure out exactly how tough your soldiers are and move in just enough troops to subdue the natives by breaking their morale rather than slaughtering them. Infantry-only often helps, as I find cavalry are too good at killing natives rather than breaking their spirit. Mid game, I often find that a 3:1 ratio of my troops to theirs is sufficient or even the most I can put in w/o a native slaughter. Late game, just a couple hundred (hundred, not thousand) infantry in the siberian corridor will break the spirit of a thousand natives. Than of course, you may want to keep the troops stationed in your colony just in case the natives have a random uprising, as if there are no troops they will damage the colony. Oh -- a minor tip, esp. in areas with big native populations -- be careful not to send that last colonist right after an uprising has been put down. It takes time for the natives to replenish their losses. After sending a dozen colonists to build up a province with low success rate but 10,000 natives, you really don't want to finally reach city statues when there are only 500 natives left...
(5) Another nasty bit to keep in mind -- enemy troops walking into your colony can and will set off a native attack against you, never against them. This can be an enormous PITA. (In my current game I have sealed the western side of the siberian corridor so Russia couldn't get in. However, every time they make war with me they rush a conquistador army, or even a regular one, into the corridor to explore -- especially after they make peace so that the army can't be attacked by me but can move under white flag anywhere in my empire. As it moves it sends off waves of uprisings everywhere, causing mass slaughter in the colonies.
I would have welcomed them, but WTF???!? 
