It is possible to apply a shader effect to a scene object, however most of the effects don't look very good at the minute. The ripple effects work quite well on scene objects though.
Check out this template
provided by Unreal. It shows the various shader effects applied to scene objects & possibly some to the screen as well (can't remember exactly what it showed off the top of my head).
As for the effects in general... no currently you can't modify them. Simon plans on creating parameters for them in a future version of the shader toolkit script so that people will be able to tweak various settings for them. The only current method would involve you having to edit the shader toolkit script itself, which requires an understanding of both Lua script & GLSL (shader language).
Hmm in regards to 2: are you talking about specifying a specific area in the scene that applies an effect to anything that enters it? I assume it would be possible, but what I wrote in the paragraph above still applies.