If all of your calibration points were diluted by the same factor, but the starting concentrations of the compounds were different, then you should use the "Concentration Multiplier" column to make the numbers work out right.
For instance, if Compound A had calibration points:
10, 20, 30, 40
and Compound B had points:
15, 30, 45, 60
then you could set the Analyte Concentration on the replicates to
1, 2, 3, 4
and set the Concentration Multiplier for Compount A to "10" and for Compound B to "15".
The Concentration Multiplier column can be found in the Doucument Grid on the view called "Peptide Quantification".
You can find that column in the View Editor at "Proteins > Peptides > Concentration Multiplier".
You cannot achieve the values in your example, since the ratio between the B and A concentrations is not the same for each replicate. Is that actually what you need?
We have not implemented support for this ability to set the "full matrix" of concentrations that vary independently across compound and replicate. The main reason for this is that nobody has sent us a dataset where they had done an experiment that required this.
That is, we have not found an experiment where there were multiple compounds with unrelated dilution series, external standards and unknown samples, and it was really necessary to specify all of the concentrations like this in order for Skyline to correctly calculate the quantities of the unknown samples.
Let me know if your dataset really requires this, and I'll see if I can implement it.
I hope the "Concentration Multiplier" turns out to be all that you need.