Question About Search Crawler Visibility

Because it is a second website under our account, our web host did not put the site’s files directly under public_html. Instead the files are in a sub-directory under public_html named after our second site. The question is whether this is likely to cause search engines not to find our site.

Second, that sub-directory then leads to the WordPress file structure. But down the line to wp-content > themes >, the name is that of a theme design that we purchased and adapted, rather than the name of our website. So same question: do we have a problem; will search engines be confused by this. What is normal for this final theme node: the (multi-word) title of the website? its URL? or doesn’t it matter?

Sorry for the weird questions but our concern is that we may have disappeared ourselves and want to tread carefully rather than screwing something up.