I’m not sure how often your wife would watch episodes over and over but you can make a playlist of the two shows. Basically filter by the two shows, sort them in aired order and then make the playlist. You can have it auto filter out watched episodes, so when she comes back to it the first item in playlist is the next episode she has not watched.
some info here Watch crossover episodes of several series in-order
(if you only have a few episode of 6MDM then personally i would just merge the files into one for those)
