Okay, I can't help with the custom init.el name, but "Can't remember how to tell emacs from Orgmode to use a differently named init file." suggests you're trying to use the org document itself as your init.el?
If thats the case, look into org-babel tangle and the auto-tangle package. You can keep the org file in Dropbox, which serves to organize elisp source code blocks that contain your configuration. With this approach, you can segment your init.el with org-mode, and add comments, links, unused older configuration, or any other info into the org document itself. When org-babel-tangle is called, the elisp source code blocks will be placed in the specified location file (look at docs for tangle on how to specify) (~/.bashrc for instance) in the order they appear in the org file.
This literate approach is AWESOME and I suggest anyone who uses org mode does it.