Do you normally keep them in the same area they are in but just move them into the corresponding "your template name" directory?
No. Copy the original file to "your_template' dir., make your edits then upload. Remember also that your Hosting directories/paths must be identical to the ones on your computer. And if you don't have a complete backup of your Zen Cart directories & files, right now would be a good time to download them.
Best to do your edits on your computer then upload the changed file. That way, you always have two complete copies in case something goes wrong. If your personal computer gets toasted your Hosting account becomes your backup. If your Hosting account gets toasted your personal computer is your backup.