Skyline allows you to fill in two different numbers in the Document Grid to specify the spiked in concentrations of peptides.
One setting is on the Replicate and is called "Analyte Concentration".
The other setting is on the Peptide and is called "Concentration Multiplier".
You should choose numbers for these two values so that the Analyte Concentration times the Concentration Multiplier is equal to the spiked in concentratrion of that peptide.
This works so long as your samples where the ratio of the spiked in peptides to each other did not vary relative to each other.
If you have a more complicated way of spiking peptides into your samples, then that is not something that is currently supported by Skyline. So far, we have not found anyone who actually needed calibration curves to enable specifying the "full matrix" of spike in quantities across peptides and replicates.
You can find more information about this in this support request: