Hosting...Domains...& SEO?

[Starting Big]

I have a hosting plan with Lunarpages, where I had an ecommerce site being developed, but now that it's about 95% done I've abandoned that project for a new site using a different URL but on the same hosting account. The new url I'm using is not the primary url on the hosting account. My question is, will running from my account's secondary domain and not having the primary domain finished effect me in any way in regards to SEO?

I hope I communicated this clearly,
Thanks,
J