How do I control the position of an indicator created with appindicator.Indicator?

The previous answer is correct in saying that the layout is like this:

  [appmenu]        [app indicators] [system indicators]

Which means you can not have the layout you mention in the question. But, you CAN move an Application Indicator within the space allocated for the application indicators. You do that by calling app_indicator_set_ordering_index() to a custom value. The value is normally generated by the application name and category, but if you want to be next to another indicator you can grab it's value and add (or subtract) one so that you are close.

It's the indicator applet's default to group application and system indicators separately, and place application indicators to the left of system indicators, so you'd probably need a modified host applet to do that.

See the specification for further information, and you can also ask for help in #ayatana on Freenode.