In the fandom section, instead of putting the fandom (like you would with Doctor Who), put "Crossover Fandom" in the fandom field instead. When you nominate your ship(s), it should look like "Character A (Fandom 1)/Character B (Fandom 2)". An example would be "Natasha Romanoff (MCU)/Leia Organa (Star Wars Original Trilogy)".

It'll then appear under "Crossover Fandom" in the tagset, which can be found under the "No Media" major category.