Starting out fresh

I am setting up a new install and I have a few very basic questions that I have not seen answers to in the docs....

I know I need to setup joomla and moodle separately but what exactly is the actual file structure on the host? Is one installed in the root and the other in a subdomain of that root? Can both be in subdomains?

I have a host setup at hostgator and currently have 16 subdomains with a main site in the root. Basically the root site is my website for my domain and it has links to each subdomain which are all different projects. Each project is a website in it's own right as I like to experiment with various CMS packages and versions. Being that I have so many subdomains running, I wanted to be sure of the structure before starting.

Also when setting up joomla and moodle, I assume it is required to use the same admin/pw combination on both so they sync?

Finally, I saw in another thread that some work is being done on making joomdle compatible with joomla3.1 how has that progressed? Is it near completion?

Thanks for your time, I look forward to checking out what sounds like a great integration between 2 outstanding pieces of software.

File structure is up to you. Usually, you would put joomla on root, and moodle on a subfolder.
Subdomains are also ok, with some restrictions (no wrapper autoheight, no redirectless SSO)

As for admin passwords: no, admins remain separate. For security reasons, Joomdle does no do SSO for admins.

There is already a public release for Joomla 3.x.