Hello,
If I understand your problem well, I think I found a solution. If your main domain is registered in yunohost domains (in the administration), then you can edit an user in the administration and chose the correct domain when defining his email address, you can also edit all the aliases. You may have to tweak your DNS configuration a bit so that mails work on main domain (I used the generated DNS config in the “Domains” menu in the admin).
Hope that will solve your problem, if not I’m afraid I can’t be of any help 