OK, Sorry, let's see if I can make it a bit easier to understand:

You will need a stills camera, one that will mount on a tripod, or if you can take single frames with your camcorder, that would work too.

You need to know how much water the glass can hold, so, let us say that is 0.5 litres you now need something that can hold 25ml of water as well.

1. set up your camera on the tripod pointing at an empty glass.
2. Take a photograph
3. Pour 25ml into the glass carefully, so you don't splash up the sides of the glass
4. Take another photograph
5. Repeat steps 3 and 4 until the glass is full (for a 0.5 litre glass this will be 25 photographs in total)
6. Make sure your photograph files are sequentially numbered: glass001.jpg, glass002.jpg, glass003.jpg, etc. , or something like that
7. Import your photos into Vagas as an image sequence (Your import menu has an check-box option for image sequence)

And now you should have a one second sequence of video with a glass filling magically.

OR
You do it sort of the way Midnight suggested BUT...

Track two has a film of the glass being filled from a jug (careful to make sure the "flow" is in the middle of the glass"
Track one has a film of the glass empty.

Use masking as per Midnight's suggestion, cutting the "pouring" image immediately above the top of the liquid in the galss (ie so the "flow" doesn't show)

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Tim