These are not specifically about structuring projects, but I would recommend two books for "thinking like a programmer". The Pragmatic Programmer, by Dave Thom

These are not specifically about structuring projects, but I would recommend two books for "thinking like a programmer". The Pragmatic Programmer, by Dave Thomas and Andy Hunt, is a fairly slim book that aims to cover the unwritten knowledge that experienced programmers have. It came out a long time ago, but it's one of those timeless classics. If you can read this book and everything in it seems obvious, you are probably the equivalent of an intermediate-level software developer. Similarly, Code Complete, by Steve McConnell, explains how to think like a project lead. In contrast to The Pragmatic Programmer, this is a large book: it aims to cover many concerns. Again, the less that you know, the more value that you will get from it: if you are starting with no training in programming, this book could be immensely valuable.