I'm designing a website which will have a large content of businesses on separated sites. Like each site would be something like: mydomain.dom/shoe-seller mydomain.dom/wilsons-fastfood mydomain.dom/flight-usa etc.. So what i'm thinking is, if those sites would get a better page rank if i added their separated URL into some SEO friendly business directory. By separate URL i mean i.e "mydomain.dom/wilsons-fastfood". So if people searched "wilsons fastfood" in Google, would it have a better page rank if it was listed? However, my website "mydomain.dom" would be already added in this same directory.
You will not get any benefits by adding your websites pages to same directory. Better you should submit your site to different directories.
That's advisable to build their own backlinks for each inner pages, not only in directories but through other method as well.
Building backlinks to separate websites on subdomains or subfolders is essential for getting them ranked for those specific keywords, yes try to add them into different directories than those where you have already added your main domain, it helps