Using WordPress in addition to an FTP program

I am responding cautiously here since I have gone as far as my own actual experience might be of any true value other than “in principle”, as such!

However….

cgi-bin is a server-rated folder that will always be empty (as far as I know) unless/until you go to your BlueHost CP and look at some specific stats…and I think you will find folders of that name in a variety of places.
Point: cgi-bin is not a WP-related folder as far as I know.

Concerning

wp-admin
wp-content
wp-includes

Each individual WP installation will have (or does already have) folders with those names in its own location, and the fact that you have them in public_html suggests to me that you have a WP installation in public_html that would be the one I have been suggesting you move into its own folder…and yes, I do understand the confusion here since you already have your sub-domain folders in place. So, that is something I would suggest getting sorted out before you might do anything else.

Concerning .htaccess
Just prior to posting here right now, I was working on my various .htaccess files where I have one (a “master”, so to speak) for public_html and then a unique-and-separate one for each of my sub-domain folders as well as even further-unique-and-separate ones for various locations within each sub-domain.
Point: Do not alter, move or copy your public_html .htaccess to anywhere else (other than locally as a backup, of course).

Concerning these:

400.shtml
401.shtml
403.shtml
404.shtml
500.php
500.shtml
default.html
favicon.ico
index.php
license.txt
readme.html
wp-activate.php
wp-blog-header.php
wp-comments-post.php
wp-config-sample.php
wp.config.php
wp-cron.php
wp-links-opml.php
wp-load.php
wp-login.php
wp-mail.php
wp-settings.php
wp-signup.php
wp0trackback.php
xmlrpc.php

I definitely recognize at least most of those files as WP files that are part of the WP installation that is also dependent upon the wp-admin wp-content wp-includes folders you presently also have inside public_html and that I have previously suggested moving. But at this moment, I do not have an answer about moving or deleting anything anywhere…and I suggest you do not until someone more knowledgeable than I has helped you be certain your clearly know and understand whether or not anything inside public_html other than .htaccess and your HTML work should be moved or deleted.

It was my understanding WP was a user-friendly program and anyone with half a brain could create a workable store and a workable blog with it. I will be finding out as soon as I catch my breath from what you and I have just been thru…whew! (Wishing I had a strong drink!)

With or without the drink, I believe you will ultimately find “user-friendly” to be true…and *especially* if you first complete this setup process with the same level of precision some of us already know proves best in the end even though we do occasionally over-think one thing or another!

Now handing you off to whomever (or maybe to whoever since I can never remember)…

Thank you Lee. I very much appreciate your honesty while helping me. I will ask BlueHost about these files and about the pros/cons to creating that new motdaugrnds folder and moving WP folders into it.

I suspect those extra files (the ones in my public_html directory yet not showing up in my sub-domain folders) are there because of the initial work I did in trying to work within the WP framewood on that main domain. I ultimately abandoned the idea of using WP to create that main domain, yet I kept WP installed. I will talk with BlueHost about this as well.

It seems practical to me to create the new motdaugrnds folder to hold what I’m not using for that domain, which is the WP program. At any rate, I’ll talk with BlueHost more about this.

Thanks again for being so patient with me. I know I can be exasperating at times; and I’m grateful you stayed with me and helped as you did.

I enjoyed the exchange and you are most welcome. I think you are going to find you can delete the WP files from public_html and lose nothing, then let BlueHost help you establish login connections (if you do not have them already) to your WP sub-domains’ logins…and then as you have mentioned, a link is a link is a link to let other folks in there. My only other thought at the moment is that you will want to also delete the database that matches the public_html WP installation, and you will do that at your BlueHost CP *after* you are first absolutely certain which database you find there belongs to which WP installation. Security will be yet another upcoming matter, of course, but one thing at a time, eh?!