Hi.
I have a google apps account with a domain and a couple more domain Alias.
I was wondering: is it possible in some way to be able to send messages as a domain alias, and use it as primary domain for a specific email or do I just need to create another google apps acc?

Yes, first you add the alias in the admin panel, then when browsing the actual gmail inbox, click on gmail settings, go to "add account" and add yourname@youralias.com, it will send a confirmation email and you just click it and it's added.
Then you can choose to use that email address as main email.