I read this book, The Perfect Mess, about the benefits of a little mess. Or said in the other way, the cost of organization.
In either way, done right, it can save you hours, days, weeks and months, done wrong it can cost you the same. Applying processes can save you a lot, but it can cost a lot as well if done wrong.
Gosh, what I want to tell you? Iterate, experiment, try and the most important point: ADAPT.
No single system is free of errors, and if a system claims to be perfect, that's the first sign that you should dump it.
Plan change, act on the change, see how it goes and adapt. Do this again, again, again and again.