Wow, good question. There are numerous tutorials, guides, web sites and other helpful tools to get you started. And each is tailored to a different goal, be it mesh design, design of surface bases, spacecraft, coding, etc. etc.
First, I'd start by playing with scenario files with the goal of learning how every little part in a scenario file works. This really helps you understand how Orbiter files work, the necessary elements in every Orbiter scenario. For example, you need a date, start location, ship or list of ships, initial state of MFD's, ships and payloads, etc. If anything's missing, the scenario will not load. Study the orbiter.log file in the root orbiter directory to see what went wrong.
Next, to do a spacecraft, for example, I see three "levels" of involvement.
1. Simple config file. Orbiter has a simple default vessel that will fly in space just fine. You can write a config file to provide the values you want for thrust, fuel, mass, size, mesh (the 3D graphic for your ship), etc. Ships have many values, but your config file can simply provide the values you care about, and Orbiter will use default values for the rest. This is probably the easiest way to start. There is a nice tutorial "Dev UFO" that explains how to do this, and also even teaches you how to make your first mesh, of a flying saucer. I'm not sure where this tutorial is, but I'd search this forum, or the Orbiter Hangar for it. Or try Google.
2. Once you've got config files figured out, move to Vinka's Spacecraft3 and multistage2 programs. Download the file packages from
http://users.swing.be/vinka/
Here, you must once again provide config files. Multistage2 is for launch vehicles, and nicely simulates boosters, staging, interstages, and handles payloads well. Spacecraft3 again lets you define a spacecraft using a config file, but this time allows other cool things such as animations (such as rotating radar dishes, engine thrust flames, unfolding solar panels, parachutes deploying, etc.) and fairly sophisticated aerodynamics. One way I like to use these two DLLs: Use multistage2 for the rocket, and spacecraft3 for the payload spacecraft (manned craft, satellite, anything).
3. Once you're really sure what you're doing, try coding your own spacecraft, writing your own DLL's. You be able to add really sophisticated capabilities, anything you can dream of.
Just my two cent's worth. I'm sure others will point you to various tutorials to help get you started
