Primary sources are reports of medical research or original documents. Secondary sources are reviews of primary sources, commentaries on primary sources, textbooks, blogs and reports by government agencies such as the CDC in the US and PHAC in Canada. Court decisions are often excellent secondary sources because a non-expert (the judge) gives reasons for the decision in language meant for other non-subject experts, lawyers, including appeal court judges who may review the decision.
Vaccination opponents love primary sources because they can cherry pick the ones they like. They may pick ones that are many years old in a field where the science and medicine keep changing. Primary sources often are written with a specific audience in mind that is expected to have technical skills and background. So quotes from primary sources may have a very different meaning to the intended audience as compared to your run of the mill vaccination opponent let alone a reader who is unversed in the topic.
Secondary sources often put primary sources into context. They explain what the primary sources mean and what is right or wrong with primary sources. They tell you the science consensus as of a certain date.
Yes, there are good ways of using primary sources. Unfortunately, vaccination opponents tend not to use them properly.