I think the way it works is that once you submit your primary to any school, you're considered a re-applicant through AADSAS. If you're asking about "applied" for specific schools, I think it's also once you submit your primary to that specific school. Not submitting a secondary if there is one would still make you an applicant but rejected for an incomplete application.
If you think about letters of recommendation, if a school requires 1 chemistry and 1 biology professor but you submit 2 biology, you've still applied but they'll probably reject you for not meeting the application requirements.
