.htaccess how to allow a folder/subdomain?

I am trying to allow a folder because I am using a knowledge base for FAQS which is its own program so have to run it with a sub domain. Ofcourse, I am able to run the main script in folder, but anytime I go to a link of course it goes back to my main site and says page can not be found. I tried RewriteCond %{REQUEST_URI} !/helpme/ and put it after rewrite engine on, but it didn't work. Am I missing something? Any help be appreciated :) 

I am not sure I follow, do you want to put Dolphin into a sub-folder and install it there with a sub-domain or do you want your Knowledge Base in a sub-folder with a sub-domain?

Yes what you said in the end. I use separate software for the knowledge base in its own folder, with its own sub domain. 

Create a folder/directory for your knowledge base in the root of your Dolphin site.  Upload the files for the knowledge base and create a database for it if it needs one.  Go to your control panel and create a sub domain for your knowledge base and point the subdomain to use the folder you created.  For example, if your Dolphin site is in /public_html and you created a folder knowledge_base then you point the sub domain to use the knowledge_base folder.  Most control panel will present you with a list of folders when you create the sub domain.  You would then install the knowledge base by using the sub-domain.

I did all this. Dolphin is blocking the folder. I had this problem with Oxwall as well and I fixed it by using the .htaccess rule I listed, but this did not work with Dolphin. I installed my software already days ago. Just trying to allow it in htaccess so it works properly. I have this problem because Dolphin is ran from the main public_html. Its jsut strange bc It allows the main page my https://helpme.secretharmonyinsl.com, but doesnt allow any of the sub directories in that directory as you can see when you click the link it will take you to the main site. Update* I rewrote a whole new htaccess file for the folder and that fixed it. Thanks