A couple sample build systems for Sublime Text 2.

Current.sublime-build

{
	// standard one, non-standalone HTML to 00-MarkdownOutput.html
	// Turabian citation style
	"cmd": ["pandoc","--smart","-o","00-MarkdownOutput.html","$file_name","--csl","C:\\Users\\Duncan\\Github\\styles\\turabian-fullnote.csl","--bibliography","C:\\Users\\Duncan\\Github\\sources\\zotero-sources.bib","--bibliography","C:\\Users\\Duncan\\Github\\sources\\bibleworks-sources.bib"],//,"--bibliography","C:\\Users\\Duncan\\Github\\sources\\logos-sources.bib"],

	
	// standalone HTML using source file name as base
	// MLA Citation style
	// "cmd": ["pandoc","--smart","-s","-o","$file_base_name.html","$file_name","--bibliography","C:\\Users\\Duncan\\Github\\sources\\zotero-sources.bib","--bibliography","C:\\Users\\Duncan\\Github\\sources\\bibleworks-sources.bib","--csl","C:\\Users\\Duncan\\Github\\styles\\modern-language-association.csl","-c","C:\\Users\\Duncan\\Dropbox\\standalone.css"],//"--bibliography","C:\\Users\\Duncan\\Github\\sources\\logos-sources.bib",

	// word docx
	// Turabian citation style
	// "cmd": ["pandoc","--smart","-s","-o","$file_base_name.docx","$file_name","--bibliography","C:\\Users\\Duncan\\Github\\sources\\zotero-sources.bib","--bibliography","C:\\Users\\Duncan\\Github\\sources\\logos-sources.bib","--bibliography","C:\\Users\\Duncan\\Github\\sources\\bibleworks-sources.bib","--csl","C:\\Users\\Duncan\\Github\\styles\\turabian-fullnote.csl"],


	"working_dir": "$file_path",
	"selector": "source.markdown.markdown"
}

variant-attempt.sublime-build

{
	"selector": "source.markdown.markdown",
	"working_dir": "$file_path",
	"cmd": ["pandoc","--smart","-o","00-MarkdownOutput.html","$file_name","--bibliography","c:\\users\\Duncan\\Dropbox\\sources.bib","--csl","c:\\users\\Duncan\\Dropbox\\turabian-fullnote.csl"],
	"name": "pandoc output HTML",

	"variants": [
		{
			"working_dir": "$file_path",
			"cmd": ["pandoc","$file_name","-o","$file_base_name.pdf"],
			"name": "pandoc Output PDF"
		}
	]
}