Choose which BSD# branch to track
First, have a look to the Branches of mono ports maintained by the BSD# Team and make yourself an idea of what you want to track.
Install portshaker
Portshaker is now in the FreeBSD ports, so installing it with a working configuration is as simple as:
make -C /usr/ports/ports-mgmt/portshaker-config install
Update your ports
Updating your FreeBSD ports tree, your copy of the BSD# repository and meging them is as easy as running portshaker:
portshaker
The default behaviour is to update and merge all configured ports tree.
Updating you ports
Since the BSD# ports tree is merged into the FreeBSD ports tree, you can update your ports the usual way (using portupgrade for example).