If the domains are created in a 'standard' fashion, then that should not be necessary, but without knowing more about your exact setup and what you did when creating domains and DNS entries, I can only 'imagine'.
For now, go ahead and add mail.domain.com into the 'rcpthosts' file.
Then in the 'virtualdomains' file, you will have to find the existing 'domain.com' and see what prefix number it has, then use the same number when adding the 'mail.domain.com'
Example: If the 'domain.com' shows as:
domain.com:14
Then add:
mail.domain.com:14
After making these edits, save them and restart the Qmail process/service.
If this does not solve your problem, you will have to post much more detail about your server, and exactly what you did when setting up the domain(s) since it appears that you may have done something not quite standard.
Also please clarify what you mean by "thats what the domains are pointing to"