If you add leaves or other object to your tree you can select the particles settings that should be associated with that particle system (in Blender the particle settings are separate entities from the particle systems themselves). The simplest way to add your own leaves would then be:

• in a separate .blend file, create a simple object, for example a cube

• add a particle system to it and give both the particle system and the particle settings a meaningful name.

• make it an Emitter type (not hair) and set start and end frames to 1 so that all particles will be shown immediately. The number of particles doesn't matter as this will be filled in by the addon.

• tweak the particle system to your specifications

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  • create a group of at least three different objects to provide some variety

  • the origin of the objects should be located near the point where a leaf attaches to a branch

  • the leaf should be oriented in the Y direction (after you have either cleared or applied any rotation. In other words it is best to rotate your mesh in edit mode):

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  • A slight amount of random rotation and phase will make your leaves look more realistic:

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  • Do not forget to UNcheck the emitter option in the render panel of your particle settings

• save the .blend file

• open the .blend file with your tree

• append the object with your particle system

• select your tree, and in the Leaves and twigs panel you should now be able to select your particle settings

You are seeing the LeafEmitter object. This probably means one of the particle systems that you selected for your tree has the emitter option checked. Uncheck it, it is located in the Render panel in the Particle options:

When you have created a good looking tree you might want to populate your scene with a few more but in reality no tree is exactly the same. Fortunately all the values used to create the tree are stored with the tree so creating a similar one is simple: select the tree, duplicate it, go to the Space Tree Pro properties and select a different random seed in the Trunks and branches panel. Now click 'Update' to create a new variant.

(Note that the trees are not rotated! each one is duplicated and given its own random seed.)

Another method is to duplicate the tree, add some small strokes with the grease pencil and update the tree with the grease pencil option selected. This method has the advantage that you can control the look of your tree variants a bit.

Probably your influence range is too low. The influence range is a multiple of the branch segment length so if its low it might not  'see' any markers.

Yes, one of the ways to do this is by adding and animating a lattice modifier. See this blog article for more on this.