If you're running php 5.2 in either cli or cgi (suphp), and would like 5.3 instead, you can do so with the following commands:
cd /usr/local/directadmin/custombuild
./build set php5_ver 5.3
./build update
./build php n
./build rewrite_confs
CustomBuild 2.0
If you're looking to change php versions in CustomBuild 2.0, say from php 5.5 to php 5.3, you'd type:
cd /usr/local/directadmin/custombuild
./build set php1_release 5.3
./build update
./build php n
./build rewrite_confs