My concern is that when applying for a Schengen Visa there is a clause that states that you need to apply with the country that is your intended destination or the country you are staying in the longest...
Your concern is correct in some ways. You file your Schengen visa application at the diplomatic mission of a Schengen state which is your the only or the main destination. When visiting several Schengen countries, the main destination constitutes the state where the stay will be the longest. If the duration of your stay in several Schengen countries is equal, then the main destination constitutes the state in which lies the main purpose of your travel. In case it is not possible to determine the main destination based on these criteria, the application is to be filed at the diplomatic mission of a Schengen State which will be visited the first. This is coded in
Chapter 3 (Short-stay visas),
Article 12 of the The Schengen acquis.
2. The contracting party responsible for
issuing such a visa shall in principle be that
of the main destination. If this cannot be
determined, the visa shall in principle be
issued by the diplomatic or consular post of
the contracting party of first entry.
and also in the
Title III (Procedures and Conditions for Issuing Visa],
Article 5 of
Regulation (EC) No 810/2009 of the European Parliament and of Council (Visa Code):
Member State competent for examining and deciding on an application
1. The Member State competent for examining and deciding on an application for a uniform visa shall be:
(a) the Member State whose territory constitutes the sole destination of the visit(s);
(b) if the visit includes more than one destination, the Member State whose territory constitutes the main destination of the visit(s) in terms of the length or purpose of stay; or
(c) if no main destination can be determined, the Member State whose external border the applicant intends to cross in order to enter the territory of the Member States.
How you define and present your travel itinerary at the border control is up to you.