I just did easy apache to upgrade my apache and php.

All went fine, but now it seems php is running as a cgi 'script'. I thought i always used the mod version. The server seems faster now (could also be apache), but i have a problem.

I cannot give php_admin flags and values in the httpd.conf anymore. Is it possible to use this with the cgi version?

The standard open_basdir config is useless now. And i also had some manual configs.

If not, how can i get php running as a module again?

you checked phpsuexec when you ran easyapache. You can run php as a module by running it again and NOT checking phpsuexec. Alternatively you can add any custom directives you want to a php.ini file for each hosting account.

My advice is:
if you are used to mod just recompile. php.ini files have been covered in depth in the cpanel forums.