You can do like the Soccer leagues with promotions and relegations. Using Raw and Smackdown as major shows or only one of them and use Nxt as the b or c show and by the end of the season promote the best of NXT to the major shows, while relegating the worst ranked in each division to NXT, acts similar to a Draft.
Since auto-booking is based on the divisions and match tables, I normally leave the title defenses for the main PLEs, while minor rivalries and storylines for the minor PLEs. And mainly "in division" rivalries and matches, similar to how's done in UFC minor PPVs, where they don't have title matches, but fighters going up and down rankings, building up for the major PPVs.
Run ins and MIB cash ins, only work in Normal matches, not custom ones. 😅 I noticed that aswell. Or if I do manually rivalries, it turns the custom matches into Normal matches.