If you are concerned that copying the entire folder from the downloaded module may overwrite files in your installation, rather copy the files from the extracted module individually into your installation.
Be sure to copy the files from the downloaded module to their corresponding locations within your installation:
The list of files needed in your online installation is as follows:
Version 3.*
wp-content\uploads\espresso\gateways\payfast\index.php wp-content\uploads\espresso\gateways\payfast\init.php wp-content\uploads\espresso\gateways\payfast\payfast.log wp-content\uploads\espresso\gateways\payfast\Payfast.php wp-content\uploads\espresso\gateways\payfast\payfast.png wp-content\uploads\espresso\gateways\payfast\payfast_common.inc wp-content\uploads\espresso\gateways\payfast\payfast_ipn.php wp-content\uploads\espresso\gateways\payfast\payfast_logo.php wp-content\uploads\espresso\gateways\payfast\payfast_vars.php wp-content\uploads\espresso\gateways\payfast\payfastlogo.gif wp-content\uploads\espresso\gateways\payfast\settings.php wp-content\uploads\espresso\gateways\payfast\LICENSE.txt
Version 4.*
[ee plugin root]\modules\gateways\PayFast\index.php [ee plugin root]\modules\gateways\PayFast\EE_PayFast.class.php.php [ee plugin root]\modules\gateways\lib\payfast_common.inc [ee plugin root]\modules\gateways\lib\payfast-logo.png [ee plugin root]\modules\gateways\lib\payments_by.png