Some companies (like Hilton) require that all charges from all rooms be placed onto the same folio in order to earn points. Marriott doesn't have that sort of restriction. Here's what it says in the Marriott Terms and Conditions:

"A Member may only earn Points for up to three (3) guest rooms during any Stay if he/she stays in one of the reserved guest rooms and pays a Qualifying Rate or redeems a Points redemption Award or a promotional Award for all of the guest rooms."
Source (section 2.1.d.i): https://www.marriott.com/loyalty/terms/default.mi

As there's really no requirement, that makes red star's answer the right one: "There is no best way."

If I were in your shoes, I'd check-in in person and make sure you explicitly tell the Front Desk representative that you want all the points. This scenario isn't an unusual one, so don't be surprised if get a simple affirmative response ("no problem").

Since fixing a problem after you've left the hotel is a huge hassle, it's probably worth taking a few minutes to stop at the Front Desk on your departure day to double-check that everything was properly done.