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first create the tree as root so s6 will look for user services for this particular user.
# 66-tree -nE boot-user
then enable the following services on say a user named jo (replace jo with your own)
# 66-enable -t boot-user -FS scandir@jo setenv@jo svscan@jo mount-run@jo dbus ....
dbus is included since it is most likely the reason you created the boot-user module so you can run user level services as dbus-user, you can add consolekit to the tree if it is needed.
Now as user:
% 66-tree -nEc jo
% 66-enable -FS dbus-session@jo xdg-user-dirs
To see if it all works run
# 66-intree -zg boot-user
% 66-intree -zg jo
# indicates a root command
% indicates a user command
# 66-all -t boot-user up
% 66-all -t jo up
If it didn't work immediately it will work on next boot, I don't know why it does this sometimes.
If it works /run/66/ will be populated correctly for user 1000 or whatever the id for the user is, s6 scans those directories for what service files to supervise. This is what the scandir initiates.
I encourage everyone to read the 66 documentation, it is not that much and in most cases it is very easy to understand if you keep experimenting and trying things live. Just don't mess with the boot@ module live.
# 66.setup
will get you back to the default initial joborun setup if you have messed up.
So go ahead and experiment and read the 66 documentation and wiki, especially the 66 introduction and FAQ,