Hi
From your post I get the impression that you are trying to put your "green screen" film on the sequence line which is incorrect. Your background (animation footage)goes on the sequence line and the "Green Screen" foreground object (your person speaking)on the overlay track. This is how I suggest you proceed. (It's a bit long so you might be best printing it out.)
Under normal circumstances you film a normal background clip (your animation in this case)against which you will place your "green screen" object/person.
So the first thing is to open VP and then add ("Add Media") your background clip (your animation) to the media list. From there you drag it to, and drop it onto, the sequence track. (You can add it to the sequence in a variety of ways but drag/drop is simpler.)So far this is a simple normal film.
Now you will need your foreground "Green Screen" clip. This can be filmed against any reasonable background colour. i.e you could use the side of a coloured building, or a single coloured sheet. It doesn't have to be pure green (or even green) but it should be reasonably uniform to work well. (Even white will work but not too well as faces have white areas.) Try not to get other items in the shot that have a different colour and its also best if the subject doesn't have anything clothing on that is near to the colour of the background or it will disappear also in the final result. (They won't become naked however 
)
So, create your clip,(your person speaking) add it to the media list and then drag/drop in onto the overlay track. Align with your sequence clip and wait while VP registers it. By default it will probably appear in the preview window (on the right) as a little image at the centre bottom.
IMPORTANT....One thing to note however.- Your person speaking will be silent as the overlay track is only a video track, it has no associated soundtrack. To get around this right click this particular clip in the media list and select to "Save audio track as a separate file". This will put the sound file in the media list from where you can drop it onto Soundtrack 1. You will have to match it up with the overlay at the end.
Now,Left click the overlay track clip so as to select it and the image will appear in the left preview window with the controls beneath it. You may have to scroll the preview window to the right to show all the controls.
Now click the centre square of the arrow matrix to centre the overlay image and then adjust the size slider so the overlay image is full size. (I am assuming it is the same size and shape as your sequence line video clip.) Now the only image you should see in either preview pane will be the overlay image. This is because it is fully opaque and it covers the sequence line video clip.
So, in the left hand preview pane,click the green chroma key button followed by the colour square. Select a colour that is closest to your chosen background colour. As you have the image present on the screen you can make a reasonable guess as to the closest shade. You can also, if you wish, create a new colour or adjust a selected shade by clicking the "Personalised colour" bar and then using the colour matrix that appears. Whichever way you select your colour-Click OK.
Next. Set the Opacity to 100% to ensure your "subject" is not a ghost image.
Now you can adjust the "Foreground" slider towards the 100% end and as this is done the colours in the overlay that correspond to your selected colour gradually become B/W checked squares. This indicates which parts of the overlay have become transparent. By adjusting both background (the sequence line)and foreground (overlay) sliders you can see what effect you are getting in the right hand preview window. However you will have to click OK after each adjustment to see the effect you have achieved.
With care you can totally remove the overlay background colour leaving your subject appearing in the foregound of the sequence clip.
If you can't totally remove the background chroma colour from your overlay try selecting a slightly different chroma colour and try again.
You will now nee to adjust the soundtrack that you added to soundtrack1 so that it matches (synchs) the overlay image. You can do this by zooming in and then gently dragging the track left or right. A bit fiddly but not too difficult.
Nat
