I think I see what you're saying. The 5' to 3' thing means that DNA/RNA is made in the 5' to 3' direction, i.e. the 5' end of the new strand (DNA or RNA) will come out of the polymerase first and the 3' end will come out last. In order to achieve this, the template is read 3' to 5', i.e. the polymerase starts at the 3' end of the template and works it's way toward the 5' end. This is the case for both DNA replication and transcription.