I searched for solutions and read many articles & blogs, I strongly desired an Amazon/Kindle solution, the majority pointed to a single solution which I eventually adopted. I was trying to keep track organized with an Excel book. I personally have some OCD issues that require my books be in some kind of order that is not primary based on who I bought it from and when.
If you have works from anyplace else, then the prospects get worse. If every book on your devices is from Amazon, then you can do some organizing at 'Your Account' > 'Manage Your Device' > 'Your Kindle Library' or by using the cloud. I am guessing you have already found Amazon's Organizing Your Kindle Content.