Thanks very much. DDE was the thing i was looking for(I am not familiar at all with SendMessage).
I have read up on it and can see i need to pass a DDE command to the following effect:
dde [dde-server] [topic] [item] [data]
dde mIRC COMMAND "" /alias data for alias
I'm having a bit of a hard time trying to find a DDE Client that I can run via windows command line to issue the DDE command to mirc - I would be grateful if anyone has any suggestions.