WordPress and PHPLinkdirectory (PHPLD) Integration

I have used PHPLD & WP scripts on few of my websites but when it comes to doing some hacks or making a plugin for these, I am relatively new to that field.

I am trying to build up a resource website for the websites which use https://www.phplinkdirectory.com script at https://www.phplinkdirectory.net/

I have integrated WordPress and PHPLD pretty well so far, but I am not able to use SEF Urls on wordpress and have to use Default option.

The Search engine friendly urls will either work for PHPLD or WP, but not both, so can someone suggest me a good way to enable search engine friendly URLs for both scripts.

Thanks,
Tony