Hi Steve,
By far the easiest way to find out what modules and their parameters do is to consult the in-app help - it explains these things in more detail, including why and when to use a mask. It seems to be exactly what you're after.
For example, clicking on the Wipe module's help button will yield the following;
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WIPE removes light pollution, gradients, vignetting and color casts from an image.
NOTE: WIPE usually does a great job unaided, however anomalies that are darker ('dark anomalies') than the galactic background (such as dead pixels, stacking artifacts, dust particles on the CCD, or terrestrial objects such as trees, mountains, etc.) may throw WIPE's gradient detection off in some cases. In case of the presence of these dark anomalies, please remove them if possible, or create a mask with the pixels of these dark anomalies set to off (i.e. non-green) - make sure none of their pixels are selected for processing.
NOTE: When a mask is used, WIPE will still wipe the complete image, but will no longer take the masked-out pixels into account while building the gradient model.
TIP: If any dark anomalies are small (e.g. dead pixels), you may use the [DARK ANOMALY FILTER] parameter.
TIP: Be sure to inspect the wiped image for halos. If you see any, chances are they are caused by a 'dark anomaly'. Maybe you missed a dead pixel or something else that is 'darker-than-the-galactic-backround'.
Then, clicking the help button for, for example, 'Dark Anomaly Headroom';
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[DARK ANOMALY HEADROOM] specifies what to do with dark anomalies found by the [DARK ANOMALY FILTER]. This parameter specifies how much headroom is re-allocated for them. More specifically it specifies how many gray levels they may take up as a percentage of the total amount of gray levels available.&lf;&lf;NOTE: this parameter only takes effect when [DARK ANOMALY FILTER] is not 'Off'. It is grayed out otherwise.
The good thing about in-app help is that the help is always up-to-date and always pertinent to the exact version someone is using, as things sometimes change between releases.
Does this address your issue at all?