I am not sure I understand your question.
When you have more than one peptide selected, or you have a protein selected, Skyline displays a graph where each peptide gets only one line on the graph.
The multi-peptide graph does not give you very many options for how it displays itself. The chromatograms for the different peptides are drawn in different colors and the colors themselves employ a shading gradient. The graph is designed to be more visually appealing rather than functional.
When we implemented the multi-peptide view we did not anticipate that it would be very useful. The thinking of the time was that it's not useful to see the chromatograms of things with different retention times plotted on the same X-axis. There have been a few requests for improvements over the years and it would probably benefit from some sort of overhaul of the design.

Are you asking about the chromatogram graph when it is displaying multiple peptides? Can you post a screenshot of what you are asking about?
-- Nick