I have already written the stored procedure for this in same database as that of YAF.

I am not sure what would be the best approach for handling this requirement. I could call my stored procedure from the YAF procedure that saves a message. i.e. in yaf_message_save or may be there is a better way of doing this.

if you only want to fill a custom table then altering the SP for the message_save would be the best option.

But don't forget no matter what changes you make always documentation everything or create a fork and commit all the changes. So when there is a new version you can always apply your changes easily.