You can use/install the same bulletproof-security.zip file for all of your websites. You will need to request an Activation Key for each website on the BPS Pro Activation page. Activation Keys are unique/different for each website. You would use the Download Key used to purchase BPS Pro to request an Activation Key. The Activation Key request steps are listed on the BPS Pro Activation page. There is also additional help information in the Blue Read Me help button on the BPS Pro Activation page.
BPS Pro upgrades can either be done by clicking the BPS Pro update now button in your WP Dashboard or you can use the BPS Pro Upload Zip installer on the BPS Pro Install / Backup menu / page.