diff --git a/docs/site/vobox_startup_scripts.md b/docs/site/vobox_startup_scripts.md
index 9fbb734ba84c089363aedf0de53779d40ca54996..83777abba4b50364f7468994fb644fe42c9c5aed 100644
--- a/docs/site/vobox_startup_scripts.md
+++ b/docs/site/vobox_startup_scripts.md
@@ -4,22 +4,24 @@ JAliEn startup scripts are used to control CE and MonaLisa services on VOboxes.
 
 # Usage
 ``` 
-Usage: jalien-vobox <Command> [<Service>]
+Usage: jalien-vobox.sh <Command> [<Service> ...]
 
 <Command> is one of: start status stop restart condrestart mlstatus check
 
-<Service> is one of: ce monalisa (defaulting to both if not specified)
+<Service> is one of: ce monalisa (defaulting to 'ce' if not specified)
 ```
 
-Running a command without specifying a service will run the command on both CE and MonaLisa services.
+Running a command without specifying a service will run the command just on the CE service.
 
 ## Configuration
 The following parameters can be overridden by defining them in `$HOME/.alien/config/version.properties` as key-value pairs, but their (unspecified) default values should usually be fine:
 
 ```
-MONALISA_HOME=<MonaLisa package location>
-MONALISA=<MonaLisa version>
-JALIEN=<JAliEn version>
+#MONALISA_HOME=<MonaLisa package location>
+#MonaLisa=yyyymmdd-r
+#jalien=x.y.z-r
+#jobagent.version=x.y.z-r
+#custom.jobagent.jar.dir=/cvmfs/alice.cern.ch/java/jar/jalien
 ```
 
 > Note: MONALISA_HOME would typically be used to specify a `local` installation. The value `install` can be used to have a default version downloaded and configured.
@@ -33,5 +35,19 @@ export MYPROXY_SERVER=myproxy.cern.ch   # only needed for MonALISA
 
 > Note: if the JAliEn CE does **not need** an X509 proxy, please ensure those variables are **not defined** for the services, to avoid false alarms in the VObox monitoring tests!
 
-> Note: the JAliEn CE needs to have a valid `VObox token` to be able to submit jobs.
+> Note: the JAliEn CE needs a valid `VObox token` (typically provided through `~/.globus/host{cert,key}.pem`) to be able to submit jobs.
+
+> Note: the JAliEn CE **may** need a valid `WLCG token` in `~/.globus/wlcg.dat` to be able to submit jobs to site CE services.
+
+## Job script customization
+
+The job script submitted by the JAliEn CE (typically `~/ALICE/tmp/agent.startup.$PID`) can be customized with one or more scripts located in the home directory:
+* `~/JA-custom-0.sh`
+  * Contents get inserted before the JAliEn environment setup.
+* `~/JA-custom-1.sh`
+  * Contents get inserted right before JAliEn is started.
+* `~/JA-custom-2.sh`
+  * Contents get inserted right after JAliEn has finished.
+
+Such customizations are in use at some sites to deal with special conditions and can also be handy for debugging.