Set the 'x' and 'y' properties of the tooltip. You can use the component's x/y position on the stage to compute them. This way you can place it anywhere on the screen.
I sort of tried this and it didnt work. In my ToolTipCreateHandler, I had...
event.toolTip = new CustomTip();
event.toolTip.y = event.toolTip.y - 200;
I sort of found a solution. I had to set the height and width properties in the MXML code of the custom component. This tells Flex how big the tooltip will be, therefore Flex knows to place it so that it doesn't go outside the visible screen. Befor, I didn't define these values so that the CustomTooltip width and height would be dependent on its children. This solution works but it stinks, if anyone has a better method please let me know.