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If you have a Skyline document where you have chosen the correct peaks for all of your molecules, you can export a spectral library using the menu item:
File > Export > Spectral Library
Skyline will put fact spectra into the library where the m/z's are the m/z's of the transitions in the document and then intensities in those spectra are the integrated peak areas from your chromatograms.
If you then use that spectral library in another Skyline document, Skyline will look at the spectra in the spectral library in order to calculate the library dot product which Skyline will use to choose the correct peaks.
Unfortunately, Skyline requires a minimum of three transitions for Skyline to calculate a library dot product. Therefore, in order for this technique to work, you would need to trick Skyline into thinking that you have more transitions than you actually do, by, for instance, adding two transitions to your document whose m/z's are almost the same (e.g. 452 and 452.001).