Good question and since I wanted to know the answer too I went hunting for it.
The answer is good news and bad news. The good news is it's all in one preferences file here: ~/Library/Preferences/org.herf.Flux.plist
The bad news is that it is saved in the binary plist data format, so chances are that if you edit it manually with a text editor then there's a good chance you'll break the file format and thus all the existing saved preferences.
If you decide to do it anyway, then make absolutely sure you make a backup copy first.
The simplest and simultaneously safest way to do this is to do this:
Open a terminal (e.g /Applications/Utilities/Terminal.app) and change to a temporary directory somewhere. For this example I use a flux specific directory in my home directory:
cd ~/dev/osxapps/flux
Copy the preferences file there:
cp -p ~/Library/Preferences/org.herf.Flux.plist .
Convert the binary plist format to XML:
plutil -convert xml1 org.herf.Flux.plist
Open the file in the text or XML editor of your choice. I usually use oXygenXML Editor for dealing with XML, but it's proprietary, very much not free and *significantly overkill for this. Emacs or Atom are more than fine for something like this situation and provides semantic display of the elements. I decided to add disable values for iBooks by inserting two lines and editing a third:
<key>disable-com.apple.iBooksX</key>
<true/>
The edited line ws just below to change the integer value for the disableCount element. It originally had five apps and now I made those lines say (only the second of these two are edited).:
<key>disableCount</key>
<integer>6</integer>
Once that's done, save the XML file as is and convert it back to the binary format:
plutil -convert binary1 org.herf.Flux.plist
Make absolutely certain you have a backup of the original file:
mkdir backups
cp -p ~/Library/Preferences/org.herf.Flux.plist backups/
ls -l backups/
Close Flux and then copy your edited version into the original file location:
cp -p org.herf.Flux.plist ~/Library/Preferences/org.herf.Flux.plist
Launch Flux again and enjoy your new settings! :)
By the way, the example I used here I was trying the first time while writing it and it worked flawlessly.