The final step is to subtract the number of excluded articles or records from the eligibility review of full-texts from the total number of articles reviewed for eligibility.
At this final stage in your PRISMA you divide your remaining articles into methodologies, and put the total number of qualitative papers into the first box, and the remaining quantitative papers into the second.
These papers are to be included in review.
Remember that your reference list will include those papers in your review, but also any information sources/ critical appraisal tools/ grey literature that you may have used.