If your main domain and sub-domain are on separate cpanel accounts then you will not be able to pipe department@domain.com to your blesta installation.
What I did was create a hidden support department (mailer@subdomain.domain.com) then create the pipe for that (in the cpanel account for your sub-domain). I then created the support departments in blesta like normal (example Support Department support@domain.com), and then create a forwarder for support@domain.com to forward to mailer@subdomain.domain.com
This seemed to work ok, blesta accepted the email, and assigned it to the correct department.
Gareth-Host Red Dragon's post in Sub Domain, Remote Mail Piping And Cloudlinux was marked as the answer