If your dilution series involves taking some high concentration mixture and diluting it with a solvent, then you should set the "Analyte Concentration" of the highest concentration Replicate to a simple number like "1" and then set the "Concentration Multiplier" on each of your different molecules to the right number so that the Concentration Multiplier multiplied by the Replicate Concentration gives you the concentration of that molecule in that replicate.
If your dilution series is something more complicated, such as mixing a high concentration pool with a low concentration pool then the "Concentration Multiplier" will not be sufficient for you to specify the concentration of each molecule in each replicate.
If you have a dilution series like that then you will need to set the "Explicit Analyte Concentration" on each of your molecules and replicates.
The Explicit Analyte Concentration can be found in the available columns of the Report Editor in the Document Grid at "Molecule Lists > Molecules > Molecule Results".
More information about the Document Grid can be found in the Custom Reports tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_custom_reports
-- Nick