Both should work, but i would advice you to enable it on the same tree mostly if you want to use a DM. To be honest, the link between a console tracker like consolekit and an user tree is not well implemented (this will change is the future).
Anyway, follow this
# 66-tree -nE boot-user # or whatever the name you want, it's up to you
# 66-enable consolekit # enable the console tracker, may be useful for complex DE like plasma
# 66-enable lxdm # this is optional, it's up to you to enable or not a DM
# 66-enable -C -F -t boot-user boot-user@ user1
# 66-env -t boot-user boot-user@ user1
the last command will allow you to configure the boot-user@ user1 service configuration file. Be sure to comment CONSOLE_TRACKER and DISPLAY_MANAGER, we have enabled its already. Also, take care of the command to launch with DESKTOP_CMDLINE if you start you desktop with startx or through .xinitrc file.
Finally, enable the boot-user@ service for the second user.
# 66-enable -C -F -t boot-user boot-user@ user2
# 66-env -t boot-user boot-user@ user2
You are the first one to ask for multiple user and this is please me :).