How do can I make my domains not show a subdirectory in the address bar for a homepage?

Hi there,

I'm really struggling with my wordpress multi-site. I have several domains that I want to run off a shared hosting. My core site works well, however any additional site asks me to put in a directory name for the homepage. I can get the sites to work ok, however the address is I obviously want to get rid of this as isn't very user friendly.

Any advice would be greatly appreciated.