dangalf,
There is a simple solution to your problem. When you have done working on your model, first save it as a ztool. Then make sure the model (or models if you have been working on several) is drawn on the canvas and then save the Document. Saving the document preserves any custom materials that are drawn on the canvas. Next time you want to work on your model, load the document you saved, then the ztool; all the custom materials will be in there right places. To continue work, clear the canvas (Ctrl+N) and proceed.
Additionally, the Material:Show Used button will show all materials in use on the canvas, Flat Color (the special ‘active’ material), and the currently selected material.
HTH,