I know of two different ways to handle this that exist in-game already.
First, there's the equipment/inventory UI. When your gear hits 100% spiritbond, the dots in the UI turn white. The alignment of the dots directly corresponds to your gear slots in your Character window, so it is not very difficult to navigate straight to the correct gear that can give you a free materia.
Second, there is the Materia Extraction/Materia Creation window. This is under Actions & Traits > General, and can be assigned to a hotbar for quick access. This is the preferred method to use if you're afraid you might "Retrieve" a materia rather than "Extract" one.