Nope BPS does not do anything with the wp-config.php or need to use the wp-config.php for anything. BPS will protect the wp-config.php file with .htaccess protection if the wp-config.php is in a publicly accessible directory. If you have moved your wp-config.php file to a protected Server directory then BPS will not see it at all, which is fine because it is already protected by doing that move.
If you already have .htaccess files/code and you want to combine your htaccess code with the BPS htaccess code then first download copies of your htaccess files as backups. And yes BPS would overwrite that .htaccess file so be sure to back it up first.
BPS has a built-in htaccess file editor on the Edit/Upload/Download tab page.
What i recommend is that you do this.
1. Make backups of your .htaccess file or files first and save them to your computer.
2. Click the AutoMagic buttons on the Security Modes page.
3. Go to the Edit/Upload/Download Tab page and click on the secure.htaccess tab. This file is the file that was created by clicking the Create secure.htaccess File button.
4. You can combine your .htaccess code into this newly created Master .htaccess file.
5. Go back to the Security Modes tab page and activate BulletProof Mode for your Root folder. What this does is copies your secure.htaccess Master file to your Root website folder and renames it to .htaccess.
Also the Read Me help buttons throughout BPS have extensive help info.