Your Questions carry a few different scenario's in it.
A: Your a theme developer and want to edit themes directly via PHP, CSS, HTML files.
Could be done.. I use CoffeeCup as my Main HTML editor and Winscp.
B: You want to load a Theme into Moodle as a plugin then make it look as you please..
Both of above can be done directly in the backend of the Bitnami\Moodle stack.. If you haven't already spend time to familiarise yourself with how to SSH and upload files via SFTP you should. As once you have a handle on this your control over your install becomes god like.. which then comes with huge responsibilities.
C: Your range of SCORM files.
Will load in to Moodle and work.. But wither this is the best way is another story.
Two options there.. Load them in as a Scorm package and or IMS content package. Both work..
I wouldn't be trying to add a theme via phpmyadmin, not the best way to try that when there are far better ways.
On that note there is a great DB plugin I have just come across that will help if you know what your doing..