Thanks, however when I manually assign clients during the installation it doesn't list any sort of site code in the config manager properties on the client and the configmgr connection type is showing as "Currently Internet" so something still is not right. I have also added the network access account from domain b sccm server to the admin group on my domain a workstation.
If i autodiscover a site code, it obviously pulls the domain a code from ad but if i manually enter the code for domain b it just says "Failed to update site assignment"