This is very much a beginner question, but I think it might help those who are just starting to use the Probe for EPMA software, because Probe for EPMA is designed completely differently than the JEOL and Cameca EPMA software.
The main point is that Probe for EPMA is intentionally designed from a "sample centric" perspective, while other EPMA software seems to be more designed from an "instrument centric" perspective. Basically when one looks at the Probe for EPMA software it appears to show a sample or samples. A sample being a collection of intensity or position data. The JEOL or Cameca software, on the other hand, appears (to me at least) to show the instrument more. Which makes sense to me because the JEOL and Cameca softwares were designed by instrument engineers, while Probe for EPMA was designed by scientists.
Basically, Probe for EPMA has two primary types of samples, each of which can contain zero to N data points. First, intensity samples (standards, unknowns and wavescans visible from the Acquire! and Analyze! windows), and second, position samples (standards, unknowns and wavescans visible from the Automate!, Digitize and Positions windows) that contain stage positions (and optionally sample conditions, setups, etc). Here is a more detailed description:
The samples in Acquire! and Analyze! windows are intensity samples (with or without intensity data). The samples in the Automate! window are position samples (with or without position data). Once intensity samples have been created and intensity data acquired (in Acquire! manually or in Automate! automatically), these intensity samples can be viewed in the Analyze! window.
You can add position data for automated acquisition from the Automate! window using the Digitize button. When you add (stage) position data to samples in the Automate! they can then be automated and then the intensity data samples will appear in the Analyze! window for quantification.
The Acquire! window only works with the "current" or last intensity sample created (usually an unknown sample). And the "current" sample can only be modified if it contains no intensity data (except changes for some background models, matrix corrections, software dead time, etc., etc.). So just create a new "current" sample if you want to change any acquisition conditions.
Remember, you cannot change sample conditions if the sample already contains intensity data (that would be unscientific!), but you can view the sample conditions from the Analyze! window using the Data, Elements/Cations and Conditions buttons.