Yeah I got a Wacom Bamboo Fun for christmas and I'm still getting used to it. Although I don't have Paint Tool Sai just yet, only corel painter and a few other random programs that came with the tablet lol.
The Opacity is to control the output density of your brush or tool, you use opacity to control the maximum pressure ^_^ and the Flow is the rate the medium is expelled from the brush or tool, how much it bleeds out when you put pressure on it .. They always work together to find a good combination for a brush stroke. ^__^