CM Remote and Digital Micrograph must never be running at the same time. CM Remote frequently gives you an error message. If the Autofilter palette shows in Digital Micrograph, click it away. The Autofilter palette is used for doing standard low-dose work with the filter and should be self explanatory. Holding down the option key when choosing some button will usually let you set the necessary parameters.
Alternate shutter means pre-specimen blanking, otherwise a blanker in the filter itself is used.
The mouse is programmed so the central button corresponds to holding down a button continuously, which is useful for opening menus, for example. In IFC, the central button corresponds to the minus button, the right one to the plus button, which is helpful for the adjustments. Don't shut off the computer. It will go to sleep by itself after about 30 minutes. You wake it up by hitting for example the space bar.