To upgrade mysql using the custombuild script, do the following:
cd /usr/local/directadmin/custombuild
Edit the options.conf file. Set:
mysql=5.1 mysql_inst=yes mysql_backup=yes
Where mysql= can be 5.1, 5.0 or 4.1.
Save/exit, then type:
./build mysql
A full raw sql backup will be run prior to the upgrade if you have mysql_backup=yes set. It goes without saying, always make backups, either with this tool, or with other means.
After the mysql update, always recompile php.
./build php n