MySQLi (I stands for Improved) has replaced MySQL which as of PHP 5.5.0 will be officially deprecated. You have already made a good decision to move to PHP / MySQL, now its just another little step to bring you right back up to date using the MySQLi extention instead. The deprecation is down to PHP upgrades not anything to do with WebAssist tools.
Fortunately, the guys at WebAssest have once again come up with a very cool extension (MySQLi Server Behaviours) which I have already purchased, tested and can tell you...it's amazing. Clean efficient code replacing the very untidy DW native code which we have had to endure for years. Don't be down hearted. Make this small (comparatively) small investment for you and your customers, you will easily recover the outlay in your first project or two.
I can tell you this, during my time as a designer / developer, I have tried many tools out there from other vendors and in all honesty, WebAssist provide consistently excellent tools, that, generally, with exception to any local configuration issues, work out of the box. I now actually only have WebAssist tools in my configuration. I got rid of the others (from other vendors) as they just do not work as they were advertised and believe me, I have spent a lot of money researching different tools and finding out for myself.
I should say, these are my own opinions and I am customer of WebAssist, have been for years and I am in no affiliated to them (as such).