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To visualise using a camera, first select a camera, then select a filter set, and then click on 'live' if the camera view isn't already showing in live. There are different sets for different uses and different cameras. Most people would use one or the other camera and not both at once. The 95B is more sensitive than the BSI, but it has larger pixels and hence lower resolution. The "Signal" sets are single emission filters and are designed to give cleaner signals with no bleedthrough and/or crosstalk. The "Fast" sets are triple or quadruple bandpass filters which cut out the excitation wavelengths, but will let bleedthrough and/or crosstalk through to the cameras. If you are doing time-lapses where speed is important, the "Fast" filters may be better, but if you want cleaner signals and don't mind the time it takes for the emission filters to switch, the "Signal" sets may be better. Details on the filters can be found here.
The stage can be controlled via the joystick (tap the bottom on top to change the speed) or via SlideBook. The "Neutral Density" filters in the focus control box aren't actually neutral density filters, but a sort-of shutter to reduce the area of illumination of the lasers so that it is closer to the field of view of the camera and doesn't bleach outside of the area you are capturing. The focus and autofocus controls will be explained in the next wiki.