If your dilution series cannot be represented by setting the Analyte Concentration values on the Replicates and the Concentration Multiplier values on the Molecules, and you need to specify the concentration for each molecule in each replicate as a separate number then you should set the "Explicit Analyte Concentration" values.

There is no way to use different Regression Fit options for different molecules. If you need to do that then you will need to have separate Skyline documents.

By the way, there is a new feature in Skyline-daily which allows you to use the calibration curve from a different molecule. That feature involves using the Document Grid to set the "Surrogate External Standard" for the molecule that does not have its own calibration curve.
-- Nick