Any area that shows the yellow-ish overlay is called "HotSpots". These are the areas (plus some off-set single spots) we covered when we sent the impulses into the room. Consequently, these are also valid areas for signal sources (most likely instruments).
The white spots show the positions we used for our Ambisonics microphones when we recorded the impulse responses. Usually the "microphone flowers" (which graphically represent the chosen number and patterns for virtual capsules) will sit directly on these spots. When you move them to different positions of the Venue Map, the Ambisonics decoding is changed according to the new relations between source and listener (read: the rotation and angles between the virtual microphone capsules will change). This is great for centring the stereo image of a stage. The IRs used in these cases stay the same, though, so there won't be different reflection patterns or the like. You will have to select different Main Mic / Secondary Mic positions to achieve this.
... maybe you just tell me what you're trying to achieve, and I'll try to outline possible solutions.