If you're going to be developing Apps with Zendesk, then you're looking in the right place. First though, please take a good read through our Getting Started Guide which will take you through the fundamentals, as well as using a working example to guide you through Apps from the ground up.
The reference guide is a complete collection of every API available to your as a Zendesk apps developer. While we do recommend reading over the entire reference guide, unlike the Getting Started Guide you do not need to understand each method we present - only those you intend to use.
There's no particular order you need to read the Reference Guide in, but why not start at the beginning.