MySQL and PHP upgrade on cPanel are very simple process, here is a list of steps that needs to be taken to upgrade these two components:
1. Login to your WHM as root;
2. Go to WHM >> Server Configuration >> Tweak Settings, scroll down to "MySQL" section, switch radio button to "5.0" and click "Save" at the bottom of the screen;
3. For this to take effect, open root level ssh session to your server and run the "/scripts/mysqlup" command, wait until installation will be completed;
4. Login to WHM as root;
5. Go to WHM >> Main >> Software >> Apache Update
6. Click on the "Load Previous Config" button (if exists);
7. Select required PHP version and PHP options that your applications may need;
8. Click "Start build" button at the bottom of the screen and wait 15-30 minutes.(depend on the connection as well)
For MySQL upgrade, you may also need to run /scripts/perlinstaller --force Bundle::DBD::mysql.
Please note that updating from a previous version of MySQL® to a later version is not automatically reversable. You should backup your databases if you think you might wish to downgrade in the future.
For php/Mysql upgrade, kindly make sure that your applications are compatible with the latest version before do the upgrading.