How do I keep the paint and clone tools from removing the background on the composition?

I am trying to remove handling  wires from a Muppet video.  I double click on the composition (mov file) and  open the layer panel.  I can get the brush, clone and eraser to work  just fine and everything looks great until I play the preview.  I can  see all my strokes on the original movie composition. For example, the white showing in the frame below.
Since I  am very new to AE, I would imagine that I am missing a setting, but it  seems like I have tried all of them and nothing is working.
I am  using CS5, version 10.  Using the normal mode and the RGBA channel on  single frame. I appreciate any help you can provide.  Thanks!

Hi Rick,
I am trying to remove handler wires that can be seen on Elmo.  This is an
assignment for an online class.  Unfortunately, I asked this question early
last week of the instructor and he has not responded.  We are required to use
the clone, paint or eraser for the exercise.  Thanks for the tip regarding the
CC Simple Wire Removal tool.  That will come in handy in the future.  The
original clip of the Muppets does have a black transparent background. I
changed the composition settings so that I could better see the wires.  Some
of the wires are just over the background and some are over a part of his
clothes.  I can see my strokes when I toggle the transparency grid.  I will
try the clone tool on the alpha channel and see if that works.  If that is not
what I should be doing, please let me know.  Thanks for your help.
I'm not really clear on what you are trying to do. If you're painting on RGBA
and you paint with a white brush you will end up with a white stroke on the
layer. All channels will be white.
 
If you're painting with a white stroke using Alpha then you will paint white
on the alpha channel so there will be nothing changed on the layer.
 
If you are painting with a black stroke using Alpha then you will paint a hole
in the layer which will allow the layer below to show through, but if you're
painting on RGB or RGBA then you'll end up with a black stroke on the image.
 
If you want to paint out the wires then you must either use the clone tool or
make the brush the same color as your background. It looks like you have a
cream colored background so your paint tool must be the same color. If you
have wires over any other color, say over the body of one of the Muppets, then
you must carefully use the clone tool. Your screenshot looks like you're just
painting with a white brush. I'm assuming that your Comp BC color is white
(not usually a good idea) and that there is really no hole in your footage.
You can check that out by clicking on the Toggle Transparency Grid or by
dropping another layer below your footage.
 
Another option to remove the wires would be to use the CC Simple Wire Removal
tool. It works amazingly well on some shots.
>

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