I know this is really annoying, but I found some way to do this. There is an alternative to evernote called "Nevernote" or "NixNote" which synchronizes with evernote. I found out about it on an evernote page telling linux users to use it instead. It has LaTeX support built into it in the linux version. Not too sure about the windows version. When I open the notes up on Evernote they look exactly the same as I had typed them out on nixnote. I know its annoying, but it helps when I have to type out really long equations and stuff.