WordPress in sub directory

Good evening,

I have my main domain and hosting, but I am in the process of setting up some additional websites within my hosting. I have not done this before so just need some advice.

I have set up a sub directory folder for my new website like this:-

http://www.main-domain.com/subdirectory

Once I have registered my new domain, I plan to point it to the new sub directory folder (I hope this is right).

However, I have noticed with my permalinks, they show as http://www.main-domain.com/subdirectory/page-name

Once I have registered my domain, will this change or do I need to make some changes to get it to be http://www.new-domain.com/page-name

Thanks in advance 🙂