From a functional point of view, both a Primary Domain name and a Secondary Domain Alias are completely interchangable. We use the term "Primary Domain" to reflect the first one we have set up. Any subsequent domain names we add later are called secondaries.
The only place where the names make a difference is in your account info on the Admin Site. For example, if you have a ".biz" domain as the primary and a ".net" set up as the secondary, the ".biz" is the one we will refer to as the real domain name if you wish to add ODBC sources or make other site changes. Any changes made to either domain name affect all domain names equally.
For example, you could set up the POP3 email address named "firstname.lastname@example.org". Once set up, you can use both "email@example.com" and "firstname.lastname@example.org" to refer to the same email user. On the mail server, any mail deliveries or pick-up's will occur on the single underlying email account named "me".
Also, ftp.domain.biz is the exact same place as ftp.domain.net for publishing and www.domain.biz is the same as www.domain.net when browsing.
So, the short answer is no, normally there is no need to change them around. If you insist, yes we can do it, but it means that we have to delete both of your domains and recreate them in a different order. In a case like this there will be some down time and you will be responsible for reloading any content once the new domains are set up. This is called an "R and R" (Remove and Replace) and there is a charge for this service. If you would like to proceed, please enter your request through the SupportCenter (http://support.alentus.com) - Submit a Ticket > "Alentus Support" department. You will receive a "stock response" that has specific questions and outlines the implications of continueing with the R&R, please respond to this email with all of the questions answered properly. Also indicate which domains you would like Aliased (Secondary Domain Alias) to the new "primary domain". Be aware that for secondary domain aliases to function properly, they must be properly registered and the registrar should point them to the Alentus Name Servers (see http://support.alentus.com).