1. Download the required updates.
  2. Extract the XS*.xsupdate files.
  3. Transfer the XS*.xsupdate files to, say, /tmp/xsup on the master.
  4. Login on the XenServer console.
  5. Delete old log files in /var/log, e.g. /bin/rm /var/log/*.gz.
  6. Create if necessary, and change directory to /tmp/xsup.
  7. Run:
    uuidlist=`for f in XS*; do xe patch-upload file-name=$f; done`
  8. Run:
    for u in $uuidlist; do xe patch-pool-apply uuid=$u; done
  9. Delete the XS*.xsupdate files from /tmp/xsup.
  10. Shutdown the running VMs and restart each node.

If you want to free some disk space by removing old patches, try:

for p in `xe patch-list --minimal | tr , ' '`; do xe patch-destroy uuid=$p; done

Note, this will also remove any pending or unapplied patches.

Also, make sure you give XenServer more than 4 GiB of disk space to dom0 when installing the system, preferably 8 GiB or even 10 GiB.