I currently have two dedicated servers being run with Web Host Manager and Cpanel. My provider has PHP installed as a CGI instead of a module. I need it installed on a module. My question is, are there things I should not be doing to the server with WHM and Cpanel installed? What will happen if I manually edit Apache's main httpd.conf file. In other words, will it be overwritten by the control panel the next time something is changed via the control panel, or will it be ok?

Customizations you make to httpd.conf should remain as you make them. From my experience, WHM will leave those alone. cPanel/WHM leave a lot of garbage in the httpd.conf, so you might actually find yourself going through and cleaning up after them. :)