What features are you talking about that appear to be missing from your addon domains?
If you're trying to edit all 3 sites in your one Microsoft Expression Web editor, I'd recommend being sure that you're logging in separately for each site. Basically don't use your primary domain's FTP information for editing your 2 addon domains.
You can login to cPanel and other the Files section click on FTP Accounts. You should notice two FTP accounts:
Notice how the first one has an incorrect path setup, it simply duplicates your home directory path. It should instead point to the directory where that addon domain's files are kept on the server.
Click on the ... in the path name to expand and edit it to be correct.
Then in Expression web just make sure you're using the full email@example.com user to connect via FTP to that addon domain.
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