You could try to have at least two ships in each sea sector for when the inevitable war comes and then later try to have several fleets of several ships in each sea sector - sounds hard, I know but if you dedicate a couple of places to ship building they'll spit them out in no time. Try and get up the tech tree as well so you can start building tougher ships like cogs quickly.

If you can get a good link to the major middle eastern ports like Antioch and then also to Venice, you're trade will be soaring in no time. Even better - try to grab Antioch via a crusade or something.

Oh and one last thing - watch out for the Spanish and keep a decent fleet or fleets at Gibraltar