suPHP does not support php_value, php_flag in .htaccess, it uses php.ini for that account. php_value and php_flag is safer as certain PHP configurations are not allowed.
Litespeed can be configured to use the per user php.ini via PHPRC environment variable in lsphp5 external app configuration.
If you want to run Apache and LSWS in parallel, you can use our "Port Offset" feature. You can change the official Apache port to something like "78" with tweek configuration in WHM, then set "Port Offset" to 2, so LSWS will run at port 80.
The same for HTTPS port.