Use /var/www/etc/icingaweb2.

Index: library/Icinga/Application/ApplicationBootstrap.php
--- library/Icinga/Application/ApplicationBootstrap.php.orig
+++ library/Icinga/Application/ApplicationBootstrap.php
@@ -168,7 +168,7 @@ abstract class ApplicationBootstrap
             if ($configDir === false) {
                 $configDir = Platform::isWindows()
                     ? $baseDir . '/config'
-                    : '/etc/icingaweb2';
+                    : dirname($baseDir) . '/etc/icingaweb2';
             }
         }
         $canonical = realpath($configDir);
@@ -193,9 +193,9 @@ 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'];
             }
         }
 
@@ -427,6 +427,9 @@ abstract class ApplicationBootstrap
         $paths = [];
 
         $configured = getenv('ICINGAWEB_MODULES_DIR');
+        if (! $configured && is_dir($this->baseDir . '/modules')) {
+            $configured = $this->baseDir . '/modules';
+        }
         if (! $configured) {
             $configured = $this->config->get('global', 'module_path', $this->baseDir . '/modules');
         }
