Which planting do I mark Interplanted, the main crop or the companion?

Only the companion: the basil, not the tomatoes. One switch on the right planting keeps your bed space honest: the main crop stays a normal planting and keeps its space, and the companion is drawn over it.

Turn on Interplanted in the companion’s Planting Details, next to Location type. Hover over the word to read what it means. See How interplanting works.