Hi Jake,
By "within" I assume you mean to run the markdown translator from within Geany.
Assuming you are running 0.18.1 or earlier.
You can do this just for markdown by adding a build settings section and a compiler command to the markdown configuration file:
[build_settings]
compiler=whatever the command you want to run is.
The Geany manual in the "Filetype definition Files" section tells you where to find the file and where to put your personal copy (don't edit the system copies even if you have the privileges to do so)
Cheers
Lex