DeAgostini models are made for beginners, have detailed color illustrated instructions, but the kits are hugely expensive. Most prominent kit makers assume you have some skills working with wood and tools, so you work mostly from plans. That's why the Amati Pinta instructions seemed confusing; it left out a lot steps they assumed you knew already. To get familiar with how to assemble wooden model ships, you have to have a couple books on model ship building, and a guide on planking a hull. A lot of information on ship model techniques can be found online. This online guide has lots of how to texts, but you have to pay for a subscription. I subscribed to it and found it well worth the money.
Wooden Ship Modelling for Dummies. You can also find tutorials on several ship modelling forums.