I'm on GoDaddys duleuxe hosting plan which allows me to host multiple sites on the same plan. I have two domains, one which is primary for the hosting plan and therefore takes the root and then a secondary which takes a sub folder. What about when Google goes to index my sites, will they see the second site as a subfolder on the primary domain and index it that way or would they index it as the root of my secondary domain. Ideally I'd like them to index it as the root of my second domain and thus have it acting as a different site entirely.
I think you have added second domain as an add on domain. It will show you as a sub folder under your main website. This is how cPanel add on domain works. But, I think it will not affect Google to track your website. Google will consider it as a root domain and all the index pages will be crawled normally.