Note that the Stage application was designed for confirming positions only, not acquisition. The Conditions, Sample Setups, File Setups buttons are for assignments only.
Now one might reasonably ask: why then is it there? And the answer is: some people like to digitize off-line on an optical microscope and also do the condition/sample assignments off-line.
However, for image/mosaic acquisition in Stage, just set the instrument conditions in PFE or on the instrument console. You can also use the Use Auto Brightness/Contrast checkbox to help compensate for variation in samples.