Choose one of 7 Factions - Lists advantages, pick one that suits your style
Choose Difficulty - default normal
Choose Naval Combat Style - default normal
Create colonies at (random per game) designated colony spots (Number of available spots depends on your difficulty. There's 7 regions and each has 3 colonies on hard, 4 colonies on medium and 5 colonies on easy) with (random per game) resources available
Recommend saving at start, sailing around to work out a nice place (or better 2) to land, then reload save.
After creating your first colony, immediately send fleet back to Europe (by clicking the Return to Home port button on ship commands). When your ship arrives, transfer as many colonists as possible to create your second colony. If you plan for the long term, you may want to have as many colonies as possible.
Keep Colony morale high to ensure a supply of colonists from Eurpoe. If you set tax rate of each colony at 9%, you will still get a bonus to morale. Aside from that, you will need buildings that increase morale, such as Churches. Keeping morale as high as possible will ensure that you have enough colonists to escort from Europe. These colonists will remain available for three months, but are constantly replaced.
Your should have a constant stream of goods back to Europe and Colonists to the New World. Sometimes you will have not enough colonists to fill the boats. Then think about soldiers and "luxury goods". Soldiers are needed to garrison colonies and man your warships, they take up cargo space. Don't pick up more soldiers than you can use, because 1) you have to pay their wages, and 2) you won't be able to put them anywhere (once you max out garrisons)). You can't discard cargo, whether it be cargo or people. So if something is full (garrison, colony, warehouse) it won't let it come off the ship. Luxury Goods (Silverware, Ironware, Silk, Salt, etc.) are goods produced in Europe - not New world, and are cheaper in Europe then Colonies. Only sell them at your colonies, not Tortuga (*DLC).
Building Ships. There are two types, Ocean and Coastal and two classes, Warship and Trader. Only Ocean vessels can get to Europe (Return to Europe button greyed). Warships get a combat advantage, carry more guns, have less cargo and are frequently faster. Recommend mixed groups (a warship guarding transports), later when you have more ships, group ships into squadrons of up to 3 fleets.
Build what you can afford, but be careful not to spend too much. If you run out of funds, it prevents you from trading between the colony and Europe. This generally means you have to delay some of the adviser's suggestions to constantly build things that might not be necessary.