There are a couple of cool tweaks that make it work well with Emacs, which has the superb markdown-mode by Jason Blevins.
First, even though the file names for markdeep should be .md.html, Emacs works best if editing is done in markdown-mode. This can be accomplished with simple header:
<!-- -*- mode: markdown; -*- -->
Second, you don't need to run markdown on the file to view it, but rather simply open it in a browser. It's easy to bring over HTML-mode's
C-c C-v binding to markdown-mode:
(define-key markdown-mode-map (kbd "C-c C-v") 'browse-url-of-buffer)
This allows a nice workflow of editing and previewing with no further adjustments, I've found.