Remote Publishing Tools Error When Connecting to Blog on Shared Hosting

Hello

I have 2 applications that I wish to use to publish to WP sites

The hosting is with HostGator and GoDaddy (the issue is the same on both)
2 WP sites in shared hosting account…

Logically I cannot leave the 2 sets of WP files in the root otherwise it would become messy

As such I have a separate directory for each WP install

When I use either tool to publish it fails to connect

The workaround after much troubleshooting is to edit WP dashboard
WordPress address (URL) – http://DOMAINNAME.com/DIRECTORY/
Site address (URL) – http://DOMAINNAME.com/DIRECTORY/

Before hand they looked like this:
WordPress address (URL) – http://DOMAINNAME.com/DIRECTORY/
Site address (URL) – http://DOMAINNAME.com/

Obviously the latter is preferred as I don’t want visitors to “see” the internal directory structure as it’s looks and feels untidy

Does anyone have a long term solution please?

Trust this reads well

Thanks

Phil