MobileOrg needs access to a file directory on a server to interact with
Emacs. With a public server, consider encrypting the files. MobileOrg
version 1.5 supports encryption for the iPhone. Org also requires
openssl installed on the local computer. To turn on encryption, set
the same password in MobileOrg and in Emacs. Set the password in the
org-mobile-use-encryption1. Note that even after MobileOrg encrypts the file contents, the
file names will remain visible on the file systems of the local computer, the
server, and the mobile device.
For a server to host files, consider options like Dropbox.com account2. On first connection, MobileOrg creates a directory MobileOrg/ on Dropbox. Pass its location to Emacs through an init file variable as follows:
(setq org-mobile-directory "~/Dropbox/MobileOrg")
Org copies files to the above directory for MobileOrg. Org also uses the same directory for sharing notes between Org and MobileOrg.
 If Emacs is configured for
safe storing of passwords, then configure the variable,
org-mobile-encryption-password; please read the docstring of that