(As I'm still fairly new to phpRunner this might be common knowledge or maybe I'm doing something horrible....;-)).
Had to customize some things for my first phpR-project that's using bootstrap.
There might be better solutions, but here's how I did it since the themes are base on Bootswatch:
-close phpRunner (don't know if this is necessary, but I'd advise to not do the below steps with your project loaded)
-Duplicate and rename your preferred Theme-Folder in phpRunner/styles/bootstrap
-GoTo www.bootstrap-live-customizer.com'>www.bootstrap-live-customizer.com/'>https://www.bootstrap-live-customizer.com'>www.bootstrap-live-customizer.com/ and load the Bootswatch-Theme your customization should be based on (use the link on top right "Select predefined theme").
-Tweak the theme in the menu on the right, you'll see a preview on the left
-When finished click on "Download" (top of screen, dropdown) & and download bootstrap.min.css
-Open the file bootstrap-theme.min.css in the folder you copied and renamed before, delete all the contents
-Open your downloaded custom bootstrap.min.css
-Copy paste all from bootstrap.min.css to bootstrap-theme.min.css, save bootstrap-theme.min.css, close the file
-start phpRunner, goto Style, you should now be able to select your new theme.
Of course you can also download the sources (Sass etc.) from bootswatch or www.bootstrap-live-customizer.com'>www.bootstrap-live-customizer.com and do the customizations with local tools and compile a min.css file.
For not to deep modifications www.bootstrap-live-customizer.com'>www.bootstrap-live-customizer.com is a real time-saver.