I know how to enable the add-on through the script but I was wondering how to run the add-on. Meaning how do i use it through a script.
Imagine there is an addon installed called "my addon". It has a couple properties to control in the toolshelf, and an operator.
The properties are all in bpy.context.scene.
In your script/addon, you can access all these properties.
You can set properties by
bpy.context.scene.my_addon_string = "hey"
And call operators
So with a combination of editing properties and running operators, you should be able to run the addon from another addon or script.