Katsu,
I'm not knowledgable in the area of SSL certs, but you can actually change an app once you've created it.
You're on OSX, so all you have to do is find the .app file in your Applications folder and right-click (control-click) it, selecting "Show Package Contents". In the Finder window that opens, navigate to
Contents/Resources/webapp/.
In that folder, you can create (or edit if they exist) the following files:
webapp.js - the JavaScript library for your app, see the wiki for particulars
webapp.css - custom CSS (applied to every page viewed, or you can use -moz-domain to limit its scope)
webapp.ini - your webapp configuration file
override.ini - I'm not sure if this is useful
Also, you can change the icon for your app by modifying these files:
Contents/Resources/webapp.icns
Contents/Resources/webapp/icons/default/webapp.icns
Regarding the SSL certificates - are you able to edit the prefs.js file for your application? It would be located in:
/Users/
[your-username]/Library/Application Support/
[webapp-name]/Profiles/
[profile-name]/prefs.js
Hope that helps.
- Jason