Sometimes modifying your system is just escape work (says the person who added a series of projects to her OmniFocus yesterday whilst “working on an essay”), sometimes it’s a signifier of an underlying problem. What I have found (which I try to stick to) is that it’s a good idea to limit fiddling with the system to a few hours a week after the weekly review. This allows me to get through the week and see what’s on my plate, and find any problems and usually let them sit for a while. I do note tweaks to the system in my system though!
As to the guides… They’re great if you only use the desktop and if you don’t mind an approach which is not necessarily what the software developers had intended. I have frequently heard that the Things guide is backward (for example) and I know the OmniFocus guide barely acknowledges the existence of the iPhone or iPad apps despite them being the most popular version of the app sold by OmniGroup.
There are usually plenty of free guides online for setting up whichever system to follow GTD, if you let us know which system you’re using (or thinking of using) I’m sure myself and others will try to offer advice!