I like the ferry, it's a pleasant alternative to flying, although the passenger gangway has been out of action at Harwich for a while, so at the moment it's a slightly awkward and surreal bus transfer for the short hop from the ferry terminal into the bowels of the ship.
At Hook of Holland (ignoring the mostly disused dead-end platform) there are two tracks through the station and the train you want leaves from the nearest one. Like ams2008dam says there's usually a train stood there when you come out of the ferry terminal - all the trains from that platform go to Schiedam Centrum and Rotterdam so just get on it, you can't really get on the wrong train.
Changing at Schiedam Centrum (go down the steps and cross to platform 5) is probably the simplest, quickest way to get to Amsterdam, but the trains here generally seem to be already quite full so I'm another one who usually changes at Rotterdam....although if you find big stations confusing then the Schiedam Centrum option is easier (but don't get off at the slightly earlier Schiedam Nieuwland stop....no connections there).
The only thing to remember if you change at Rotterdam is that the rail ticket you get is not valid on the "Intercity Direct" trains (these are the quicker trains via the new high-speed line) unless you buy a supplement [a.k.a "toeslag" - great Dutch word] before you get on (about €2.50 or so). Also don't try and get on any "Thalys" trains. Just get a normal "Intercity" (not "Intercity Direct") train heading to Amsterdam (it tells you the type of train on the platform screens).
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Probably not worth going for the rail option if you're pre-booking with Stena
It's good value if you need the rail part within the UK - the rail/sail ticket is valid on the UK side from either London or any "Greater Anglia" station (e.g Cambridge).
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The rail tickets you get are day passes so you can literally go anywhere in Holland for that first day. Remember to swipe them though like you would an OV-Chipkaart.
Yeah, remember to touch it against one of the OV-Chipkaart readers on the platform at Hook-of-Holland before you get on the train, or get a lecture from the train guard. Because it's a day ticket, I think you only really need to touch-in, after that you can forget about it, it will stay valid to the end of the day.