How do i add a new checkbox in message template
You'll need to create an extension - see https://docs.civicrm.org/dev/en/latest/extensions/ to get started, and then you'll want to look at https://docs.civicrm.org/dev/en/latest/hooks/hook_civicrm_buildForm/ to add the checkbox and then https://docs.civicrm.org/dev/en/latest/hooks/hook_civicrm_postProcess/ to actually do something with it when the form is saved.

But also because the upload documents section is in a hidden section until you click the radio, if you want to add the checkbox in the same section you'll also need to look at https://docs.civicrm.org/dev/en/latest/framework/region/#region-reference to put it in the right place, or maybe insert some javascript there that also hides/shows your checkbox when the radio is clicked.