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So the problem is I’m not used to FTP clients and managing files with apps and directories. Webfaction has you connect to the domain and server (username.webfactional.com; listen to port 22) and once your in, you see the files already there (like bin, lib, webapp->django, etc). What I don’t get is how do I get my source code files uploaded so that they appear on my domain (cooldomainname.com)?
I think the part you are missing here is how WebFaction lays out the structure for your account, applications, and web sites. You can see some of the ways they set things up here:
http://docs.webfaction.com/user-guide/examples.html
The answer to your question is:
You need to put the files, depending on the file type (if it is static or php and you have an Static/CGI/PHP application set up), in the /home/username/webapps/appname directory. You can view your apps by looking through the information in the WebFaction docs and following them through their control panel to the information you need.