Simply click the "Archive" button at the top of a student's transcript to move it to the archive. Once in the archive, the transcript won't affect your active transcript limit. Archived transcripts can be printed, exported, duplicated, and deleted. They can also be un-archived if you need to edit them for any reason, but will count towards your active transcript limit again while you are editing.
Archived transcripts can be found in the "My Students" section of your account. They won't show up in the drop-down list of your active transcripts, which makes managing your current transcripts easier. Your archived transcripts are stored out of the way of your active transcripts, but still easily accessed whenever you need.