About ArcReader Markup
Markup allows ArcReader users to collaborate with the author of the published map. Just like one can write on a paper map, the ArcReader markup pen can be used to create freehand graphics on a published map. This digital ink is written to a published map ink file (.pmfinkx). The PMFINKX file is a companion file to the published map. Authors of the published map can open the PMFINKX file in ArcMap to view with the ArcMap document that was published to ArcReader.
Things to consider when publishing maps that will be marked up
Markups are designed to point out errors on the map. Often, the errors have something to do with text on the map. ArcMap has automatic clash detection for labels and graphics. If the map is published with the default label weight ranking for the default graphics layer, the labels in the published map will move when an ArcReader user marks them up with the ArcReader pen tool. To keep this from happening, one can convert the labels to graphics or set the feature weight for the <Default> graphics layer to none. Use Label Weight Ranking on the Labeling toolbar to make this change.
If multiple ArcReader users will be providing markup files to the map publisher, it will be important to coordinate the naming of the files and perhaps the color of the ink used by each contributor. Multiple PMFINKX files can be viewed in ArcMap at the same time, but it will be easier to discern who the markups are from when viewing if unique file names and colors are used.