My rule regarding the use of color in reports, i.e. that it color must provide information, applies to Mathcad documents also. However, with Mathcad documents, there are more opportunities for using color.
A Mathcad document is also a program that might be intended for use by others. In addition, the program author may need to use the program again much later with different input values. Color can be used to call attention to all of the input requirements. If all of the input is highlighted, then the user is less likely to overlook values that need changing.
You may think that all of the input should be grouped in one section at the beginning of the document, but that is not always the most efficient way of designing the program. Often there is a need to run several cases of just a portion of the program. In that case, it is more efficient to place the input that is to be changed for that section at the beginning of the section to avoid recalculation of the entire program. This also reduces the amount of scrolling needed to run the cases.
I use background highlights of input statements rather than changing the font color. I think the highlight is more easily noticed. Use light shades of color so the characters can be seen easily in the highlighted region.
In some cases, a single color (I use green) may be used for all input. In that case, the information provided by the color is "hey, look at me". In other cases, there may be classes of input. By assigning a different color to each class, additional information is transmitted. For example, a model of an oil pipeline involves a description of (1) the pipeline, (2) the oil, and (3) the operating environment and conditions. A color is assigned to each input class. Near the top of the worksheet, the color code is provided to the user by example:
This arrangement makes it easy to find all of the input for the changes being considered. During design of the pipeline, variations will probably be explored in all three classes. After the pipeline is built, changes may occur in just the last two classes.
The red and yellow colors might have to be changed if you use them elsewhere in the worksheet, as discussed in the next section.
Other important information to highlight
Some worksheets contain critical assumptions or directions for proper use of the worksheet. In those cases, I will highlight the critical statements, usually with red as a warning. Whatever color is used for warnings, it should be reserved for that use alone to preserve the meaning of the color.
I have also use a two color system for important information. I use red for the critical warnings, and yellow for non-critical yet still important cautionary information. Those colors correspond to the U.S. highway signage coloring standards which further makes the worksheet easy to comprehend.
If you use color for headings "just to make the worksheet look good", then the other, more important, uses of color will lose their effectiveness by being less noticeable.