I have just installed SCCM on a server at one of our branch offices and selected Secondary site and provided Primary site details etc and all seemed to be successful. However it is not showing in the Primary Site console at all... What have I missed here? Any help appreciated.

I assume that you already refreshed or closed and re-opened the console. See sender.log on the secondary. There's a high chance that the site isn't able to send data to the primary (access denied, because the secondary site's computer account was not added to the appropriate group on the primary).

check the sender.log file on the child site to see if there are any permission related errors.Kent Agerlund | http://scug.dk/members/Agerlund/default.aspx | The Danish community for System Center products

Make sure the secondary site server is a member of the group SMS_SiteToSiteConnection_<SiteCode> on the primary site server and vice versa.

I decided to uninstall and push out the secondary site server from the primary site server and it all worked perfectly that time - not sure why. I had already added the computer account to the local admins group. Yes I had refreshed console and given it a few hours even - there was simply no sign of it in there. Very strange...