The way to specify which are the standards and blanks, etc. is by using the Document Grid.
You can show the Document Grid with the "View > Document Grid" menu item. (In Skyline-daily, that menu item has been moved to "View > Live Reports > Document Grid")
If you choose "Replicates" from the "Reports" dropdown at the top of the Document Grid you will be able to fill in the "Sample Type" and "Analyte Concentration" values for each of your replicates.

Here is the tutorial for doing calibration curves in Skyline:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_absolute_quant

If you go to the "Quantification" tab at:
Settings > Peptide Settings
you will be able to tell Skyline to calculate the LOD by adding some multiple of the blanks' standard deviation to their mean.
In order to calculate the LOD from the blanks, you would also need to have a calibration curve from internal standards, since Skyline needs a way to convert the observed intensities of the blanks into an absolute quantity.

In Skyline-daily we have made improvements to the way that the limits of detection and quantification are calculated if you have chosen "Bilinear" as the regression method. In this new way, Skyline calculates multiple (bootstrap) calibration curves which use random subsets of the internal standard data points and calculates the limits of detection and quantification based on the observed variations of those curves.
-- Nick