Yes, you could do that, but ideally you would want to install BPS on each WordPress site so that you have all the tools and features in BPS. If you have a Network/Multisite installation of WordPress then BPS is only activated on the Primary site (not Network Activated) and not all the subsites.
If you have standard single site installations of WordPress then the only thing you would need to manually modify would be your RewriteBase and RewriteRules to match the sites base folder. This is one of the things that AutoMagic does automatically when you click the AutoMagic buttons.
but if you wanted to do this manually here is an example:
if you have a WordPress site installed in /FolderA you would need to edit the Root .htacces file for that site.
your RewriteBase would be RewriteBase /FolderA/ and your RewriteRules would be RewriteRule . /FolderA/index.php [L]
The wp-admin .htaccess file will work on any/all sites without having to make any modifications.