To manually set a Global Domain Controller to your BES server (version 5+), there are two settings you will need to change and add. One is to add an entry into your BES server registry. Another is to change the component settings on the BES Administrative Web Console Menu.
Read the two links below for instructions to modify these.
Remember, with these settings set, BES will no longer be able to find other GDC if the one you set is down. You will need to manually set this.