Okay, I have inserted all the files of my domains in one primary domain I have added while purchasing hosting. Now, how can I separate them? like my primary domain is xyz.com and I have two other domains abc.com and pqr.com. I have put the files of abc and pqr in abc. We get the option to separate them while adding a domain in the addon.
what files? The domains should have no files if there's no website / script set up on them, and there should be no website / script set up on them when you 1st buy them. I genuinely don't know what you're on about, so I can't help you...
In general, the process goes like this:
1) you buy domain from whichever registrar (Namecheap, Namesilo, Porkbun, Godaddy if you're masochistic, etc...)
2) then you log into the account that you have with the company that you purchased the domain from and go to "Nameservers" and type the (usually 2, but can be 3 or 4 sometimes) nameservers that the hosting company gave you when you purchased a hosting plan, into their fields and you click on "update nameservers"
3) then, after you've updated the nameservers you log into your cpanel (at your hosting company, NOT at your domain registrar, of course), go to Addon Domains, and add your domain name in there and click on update / save
4) done! You can now install Wordpress (or whichever site / script you want) onto your domain and use it normally, and after you install whatever you want on your domain you will have files.
But until you install a website / script your domain should have no file in its respective folder... well, sometimes there's a thing called "cgi.bin" in there, but that's literally the only thing you should see in that folder.
Again, I have no idea what files you are talking about, but if you want you can PM a screenshot or something and I'll see if I can figure out what you're trying to do