Cheetah and Pegasus both provide the option to have your data displayed, and record, with the Input Inverted. By default, this setting is selected on in the Acquisition Entities Properties window. This setting, in general, can sometimes lead to much confusion.
The natural depolarization of a neuron is a negative value. This would mean that the voltage change is in fact negative, and would go "down" on a typical display where up is (+) and down is (-). If you uncheck the input inverted option, then the previous sentence holds true. When you do select the input inverted option (selected by default), then the depolarization goes up. In this case, (-) is in the upward direction and (+) is in the downward.
When viewing CSC's, continuous channels, the direction of the depolarization is really up to you and how you want to visualize (and record) the data. With the spike entities, the same principles apply. Having said that, it is very critical that you change your threshold to a negative value (i.e.: 45uV to -45uV) when you Do Not select input inverted. If you do not have your threshold set to a negative value with the option deselected, then the software is attempting to identify a spike with a threshold crossing that will likely never occur, or pickup the trailing edge of the spike.
Best practice is to keep both CSC and spike entities Input Inverted setting the same to avoid any further confusion. It is also a good idea to save your custom settings to ensure no changes occur during your recording trials.