It's hard to be specific without knowing what/when you're trying to book, but as you click through each of the available options at marriott.com the total amount of MRP's that you're seeing for a stay should eventually include the base rate plus whatever upgrade certs are required.
On marriott.com, input your desired dates/location and the page that comes up will show any available rooms/units with the base rates according to the hotel/resort category. You must click "Continue" on each option to get the total MRP required for each option. You can then click on "About this rate" for any of those options to get the breakdown.
For example, 1/12-16/15 at Barony Beach Club requires 180,000 MRP, which is 140,000 base (Category 7 at 35,000 per night for 4 nights) plus 40,000 (2 upgrade certs per night @ 5,000 ea.)
Like others have said, the system will deduct the total required MRP for your stay and the e-certs will be issued automatically.
Note the base rates for any Vacation Club properties are based on studio-size units and the hotel/resort category of the property. Each additional bedroom will require one 5,000 MRP upgrade cert per night, even at the resorts which do not have studio units.