separate location for project file

I'm managing a website using byethost's free hosting. Setting up the 
project the first time was no problem.

Then I made a sub domain.

The tree for the website is now as follows:

/
/htdocs
/support.byethost.com
/support.byethost.com/htdocs
/docs.byethost.com
/docs.byethost.com/htdocs

I would like everything to be in one project.
The catch is that I don't have write permissions on the folder "/"
Can I put the project for the whole site in the folder "/htdocs" and not 
have to do a separate project for each sub-domain?

-Isaac