Netbanx only need a reference number and an amount sent to their CGI script. From this they will process the amount through their system and return a page either confirming or denying payment.
From here they will send you an email with the reference number and the amount paid.
You can send other variables through to them and these will get returned in the email.
It's awkward, because the confirmation pages are on their servers. So you will have to speak to them to see if they will send back a script to your server to update your database.
But as far as PHP and mySQL are concerned, it won't really matter. You can send the details from a form made in just html. If you build your pages in PHP and mySQL it will be easy to plug into their system. You will just have to create a couple of templates in your design for them to integrate into their CGI scripts.
I built a shop in ASP and Access, integrated it into Netbanx, then rebuilt it using PHP and mySQL and did not need to do a thing to keep it on Netbanx. I didn't even have to inform them. As long as they get the details from the form they are happy.
Hope this helps