This article applies to both PHPRunner and ASPRunner.NET.

Windows

PHPRunner

PHPRunner installs into the C:\Users\<username>\AppData\Local\PHPRunner11 directory. Many find it beneficial to modify PHPRunner files to add new languages, custom themes, plugins etc. However each PHPRunner update completely erases added or modified files and replaces them with standard ones. To make your modifications persistent save them to C:\Users\<username>\AppData\Roaming\phprunner\resources directory instead

Custom themes
https://asprunner.com/forums/topic/26144-modifyingcreating-a-new-bootstrap-theme/

You can find existing standard themes in this directory
C:\Users\<username>\AppData\Local\PHPRunner11\app-11.x.x\resources\styles\less\bootswatch

However when creating your own, save it to
C:\Users\<username>\AppData\Roaming\phprunner\resources\styles\less\bootswatch

Multilanguage messages
Standard language messages are stored in
C:\Users\<username>\AppData\Local\PHPRunner11\app-11.x.x\resources\lang
If you need to modify any of the files, first copy them to C:\Users\<username>\AppData\Roaming\phprunner\resources\lang and edit them there. Add new files also to that directory.

Rich text editor plugins
https://xlinesoft.com/phprunner/docs/rich_text_editor_plugins.htm

Unzip downloaded RTE editor plugins to
C:\Users\<username>\AppData\Roaming\phprunner\resources\source\plugins

Modified source PHP and other files
If you need to change the code of a source .php file, say menu.php, the best way to do this is to add the original menu.php file to the Custom Files folder on the Style Screen in PHPRunner, then edit it there. This way you'll have the modified menu.php file in your built application. However, if you want to apply the modification to all your projects, then copy the original menu.php to C:\Users\<username>\AppData\Roaming\phprunner\resources\source and change it there.
If you need to modify files from a subdirectory, then create the required subdirectories in C:\Users\<username>\AppData\Roaming\phprunner\resources\source and copy your files there.

ASPRunner.NET
The same applies to ASPRunner.NET. The directory where the app is installed is
C:\Users\<username>\AppData\Local\ASPRunnerNet11

The directory where new and modified files should be placed:
C:\Users\<username>\AppData\Roaming\asprunner\resources

PHPRunner MultiDeveloper Edition

The directory where the app is installed is
C:\Users\<username>\AppData\Local\PHPRunner11MultiDev

The directory where new and modified files should be put:
C:\Users\<username>\AppData\Roaming\phprunnerMultiDev\resources

ASPRunner.NET MultiDeveloper Edition

The directory where the app is installed is
C:\Users\<username>\AppData\Local\ASPRunnerNet11MultiDev
The directory where new and modified files should be put:
C:\Users\<username>\AppData\Roaming\asprunnerMultiDev\resources

Mac

PHPRunner

The directory where the app is installed in
/Applications/PHPRunner 11 Enterprise.app/Contents/Resources/
I.e.
Languages:
/Applications/PHPRunner 11 Enterprise.app/Contents/Resources/lang
Source files:
/Applications/PHPRunner 11 Enterprise.app/Contents/Resources/source
RTE plugins:
/Users/<username>/Library/phprunner/resources/source/plugins

The directory where new and modified files should be put:
/Users/<username>/Library/phprunner/resources