Linking the right blog location to WordPress.com

I have a self-hosted WordPress blog located at https://www.skepticalraptor.com/skepticalraptorblog.php
However, the files are actually located at https://www.skepticalraptor.com/blog

I had to do separate the name, because I use a web design software, where WordPress is embedded into one page using a plug-in for my software. It works perfectly. However, I want to do a few things using my WordPress.com account, like re-blogging, entering comments, etc. Unfortunately, JetPack has linked my blog’s file location to WordPress.com, not the actual location of the blog (with the .php modifier). So, if I try the re-blogging feature, it posts to the /blog location, which is hidden, and no one will see it. IN fact, if click on the re-blogging link, it gives a 404 error. Luckily, you can click on a link on that page, which will redirect to my blog’s home page, but the re-blogging attempt is not on that page (in fact, I don’t even know where it’s located).

I’ve tried to re-setup JetPack, but it insists on using the /blog location rather than the /skepticalraptorblog.php location. I could have combined the locations when I first set everything up and I forget the reason WHY I even thought it was a good idea, but now everything is messed up. My Dashboard seems to do everything right, just this one silly thing.

So, how do I correct the right blog to my WordPress.com account? Maybe I’m up the creek without my paddle, I’ll just give up on it. Maybe I’m doing one silly thing wrong. Any help would be appreciated.