One word of warning as you read through this Guide: Like too much Open Source software out there, the SCons documentation isn't always kept up-to-date with the available features. In other words, there's a lot that SCons can do that isn't yet covered in this User's Guide. (Come to think of it, that also describes a lot of proprietary software, doesn't it?)
Although this User's Guide isn't as complete as we'd like it to be, our development process does emphasize making sure that the SCons man page is kept up-to-date with new features. So if you're trying to figure out how to do something that SCons supports but can't find enough (or any) information here, it would be worth your while to look at the man page to see if the information is covered there. And if you do, maybe you'd even consider contributing a section to the User's Guide so the next person looking for that information won't have to go through the same thing...?