Oops, I missed the part about that you were using small molecules.
For small molecules, "Import > Peptide Search" and "Settings > Peptide Settings > Library > Build" will not work.
One way to create a spectral library for small molecules would be, after you have extracted chromatograms, to use the Skyline menu item:
File > Export > Library
That will create a .blib file with "spectra" in it where the "intensities" in the spectra are based on the chromatogram peak areas.
Exporting a spectral library in that way would be useful if you wanted to create a library that would be used for improving peak picking by telling Skyline what to expect the relative transition peak areas to be.
I don't think that a spectral library exported in that way would be helpful for what you want to do in terms of retention time alignment.
We might be able to give you better answers if you send us your Skyline document.
In Skyline you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms and spectral libraries.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here: