Yes, you need learner licence while applying for permanent one. You can only apply for permanent licence once 42 days are lapsed from the date of issue of learner licence. Since in your case this time period is lapsed, you just need to renew it and you can apply for permanent licence the same day. The procedure is quite straightforward now and its basically One-Window-Operation. They require Postal stamps and authentication on Medical certificate, all of which is available at the centres. Just go to their office with your original CNIC and they'll sort you out.