You mean a sub*folder* of the domain? because if you have a subdomain, and your wordpress setup is within the subdomain, then it shouldn't be showing your regular domain name.
I know that's not very clear, but I'll give you an example. I have two websites: my old business site is
www.foolishvisions.com (don't worry - not a plug for advertising - I no longer accept clients through that site, and I'm currently working to convert it to a personal blog - using WordPress!). I have a CSS site,
www.anekostudios.com. In all actuality, my anekostudios.com site is actually a subfolder of my foolishvisions.com area (in other words, you could bring it up by putting in "http://www.foolishvisions.com/aneko/". Now, if I left it like that, then even using a relative path for stuff would still reveal that the URL is what you see right there - showing the end users my upper level domain name.
To keep that from happening, I had to buy the "anekostudios.com" domain name, log into my host's cPanel and associate the domain name with the subfolder. Thus, all relative paths now point to the subdomain name, even though the files are actually lodged in a subdomain *folder*.
So, that's why I question if you're actually using a subdomain...it sounds like you're just using a subfolder with no association to a domain name.
If I'm wrong, then there's soemthing not set right on your server - because if you *are* using a subdomain name, and your wordpress install is located within that subdomain area, then the URLs should be pointing to the folders within the subfolder - not the main account. (I hope that made sense!)