The builder and flashcards contain the same list of words :) You can use both, of course, but you should be conscious about how to use them.
The Vocab Builder lets you choose the correct definition from a list of options, which makes it faster and easier to work through. That said, choosing from among answer choices does not require you to know the words as well as does recalling the definition on your own.
With that in mind, if you want to use both the Builder and the flashcards, I recommend using the Vocab Builder to help learn the words. Afterwards, use the flashcards to test your mastery.
Otherwise, use only the flashcards.
Using only the Vocab Builder won't help you learn the words as well as using the flashcards, because you'll always have the correct definition given to you among the choices. You won't have that on the test, so this isn't a good reflection of what will be required of you come test day.