When making an assessment in the tool, it is an annual footprint of a crop, but also of a specific growing area. When you grow different crops in a rotation, the different crops that follow each other need to be assessed individually and separately. You should indicate all related practices, soil characteristics etc. for a specific crop as well as the growing area on which it is cultivated.
If you grow different crops on the same field, you can use the function “save as” to duplicate the assessment of one crop, and consequently change the entries to the new crop that is on this field (make sure e.g. to indicate the used area for crop, reset the residue amount and represent the cultivation practices for the new crop). Finally, the most interesting part is the land management: if you use cover crops or tilling in your rotation, this is the only thing that needs special care. Please see the relevant questions in this FAQ. Once you assessed the different crops, you can combine the footprints offline to get a picture of the emissions of this rotation.
Even if we do not include any methodology of the positive effect of rotation in the tool, you will be able to record e.g. changes in the SOM due to rotational practices, and thus indirectly monitor the positive effects of your practices on your soil.