Hostgator Subdomains...

I purchased 2 domains (domainA.com & domainB.com) through Namecheap and will be hosting them on Hostgator, because it allows me to host unlimited domains. When I was going through the Hostgator ordering process, it asked me for my (main) domain name. I used domainA.com.

I have added domainB.com as an addon domain but have noticed that it adds it as a subdomain. I can still access it as http://domainB.com but it shows up as a subdirectory in my FTP program.

My question is, does this affect SEO in any way? Having it show up as a "subdomain" even though I can still access it directly (http://domainB.com). I guess I can always pay the $5 to have domainB.com be my "main" domain, but I just thought I'd check here first before doing any of that.

I already contacted Hostgator but they could not help with my SEO question. They just said that my addon domain is also considered a subdomain.

Please let me know if anyone needs any clarification...it's late

Thank you.

It will not affect SEO.
Hostgator needs to set it up this way when you are using their shared hosting. But google will see them as two different domains. I have over 20 domains added this on one of my hostgator accounts and they get ranked well on google.