The catalogue is a simple way to keep track of the work that has been done on groups of tomograms. This work normally aims at the definition of positions (and possibly orientations) inside each tomogram, so that subvolumes can be defined and cropped, to produce an unique data folder with its corresponding table that can be feed into a project for alignment or classification.
If you have already a set of subtomograms, you have already all the initial orientations you could reasonably extract from the tomograms and you don't want to extract the tomograms again, you probably don't need to define a catalogue. You already have all you need to start designing alignment projects.
Keeping a catalogue is not necessary for cropping particles out of your tomograms. The tools associated with the catalogue can easily be used independently at any stage. We however encourage you to organize your tomograms in a catalogue from the very beginning, as this induces a very smooth workflow and eliminates lengthy administrative overheads that are prone to happen on a later stage.