I guess you mean your designed templates. I don't think you can just copy the directories. You need to do a proper install. If you wanted save yoru templates, then follow these steps: Library --> Tools --> Export and the system will export your chosen template in the C:\Program Files\SEC\MagicInfo Pro\Export directory and the filename has .scp extention.
You need to copy this file. Its size depends on the content and then you have your template. To install again, follwo the same process on your new installation and then choose Imprt as opposed to export.
Bill