Hi Johnver,
Thanks for posting your question. I'm more than happy to assist you. No, you do not delete the installation folder. Anytime you upgrade OpenCart, you'll need to run the installer again. If you delete the folder, you'll have to re-install it. Here's our guide on installing vQmod:
Installing vQmod on OpenCart
If you need further assistance please feel free to contact us.
Thanks!
Tim S