You can apply a GPO to an OU or a site. The site GPO will be applied first and will be overriden by the OU GPO
You can block that application of the GPO to the servers OU using Block Inheritence setting but that will block all GPOs set at a higher level. If you need them to apply you need to use Override then to force the application. Might be better to apply the GPO to each of the Child OUs you want rather than to the root.