MobileOrg needs to interact with Emacs through a directory on
a server. If you are using a public server, you should consider
to encrypt the files that are uploaded to the server. This can be
done with Org-mode 7.02 and with MobileOrg 1.5 (iPhone
version), and you need an openssl installation on your system. To turn
on encryption, set a password in MobileOrg and, on the
Emacs side, configure the variable
org-mobile-use-encryption1.
The easiest way to create that directory is to use a free Dropbox.com account2. When MobileOrg first connects to your Dropbox, it will create a directory MobileOrg inside the Dropbox. After the directory has been created, tell Emacs about it:
(setq org-mobile-directory "~/Dropbox/MobileOrg")
Org-mode has commands to put files for MobileOrg into that directory, and to read captured notes from there.
[1] If you can safely store the password in
your Emacs setup, you might also want to configure
org-mobile-encryption-password. Please read the
docstring of that variable. Note that encryption will apply
only to the contents of the .org files. The file names themselves will
remain visible.
[2] If you cannot use Dropbox, or if your version of MobileOrg does not support it, you can use a webdav server. For more information, check out the documentation of MobileOrg and also this FAQ entry.