Use /var/www/etc/icingaweb2.

Index: library/Icinga/Application/ApplicationBootstrap.php
--- library/Icinga/Application/ApplicationBootstrap.php.orig
+++ library/Icinga/Application/ApplicationBootstrap.php
@@ -175,7 +175,7 @@ abstract class ApplicationBootstrap
             if ($configDir === false) {
                 $configDir = Platform::isWindows()
                     ? $baseDir . '/config'
-                    : '/etc/icingaweb2';
+                    : dirname($baseDir) . '/etc/icingaweb2';
             }
         }
         $canonical = realpath($configDir);
@@ -200,9 +200,9 @@ abstract class ApplicationBootstrap
                     explode(':', $libraryPaths)
                 ), 'is_dir');
             } else {
-                $this->libraryPaths = is_dir('/usr/share/icinga-php')
-                    ? ['/usr/share/icinga-php']
-                    : [];
+                $this->libraryPaths = is_dir('/var/www/icinga-php')
+                    ? ['/var/www/icinga-php']
+                    : ['/icinga-php'];
             }
         }
 
