You need to meet with your professor to talk about the expectations for the assignment.

Great advice to talk with your professor. That said, if it is the case that you "have been instructed to only use secondary sources in a paper", then you are not likely to have used primary sources. If you did not use primary sources, you are safest only citing the secondary sources - and that would seem consistent with the instructions as described. But if you are able, go talk with your professor.