There is nothing wrong with doing "Edit > Insert > Peptides" to get peptides into your document that were not in your spectral library.
Skyline is not going to know which charge states and precursors to choose for those peptides, so you might need to right-click on them in the Targets tree and use the menu item "Pick Children".
I am not sure why you would want to add these peptides to a spectral library. In order to add peptides to a spectral library you need to have some way of specifying what the spectra for these peptides would look like.
After you have extracted chromatograms in your Skyline document, you can use the menu item "File > Export > Spectral Library". This will create a .blib file containing all of the peptides in your document, and the "spectra" in the library use the m/z's from the transitions in your document and the "intensities" in those spectra are the integrated peak areas from the chromatogram.
If you want to merge this exported .blib file with the .blib file that you already have, you can go to:
Settings > Peptide Settings > Library > Build
and then, as input files, instead of using peptide search results, you can use the two .blib files that you already have.
If you want to create a spectral library from a list of peptides, you can use the "spectrum sequence list" format (.ssl), which is specified here:
However, in order to use this .ssl format, you would need to specify which spectrum from your raw files Skyline should put in the spectral library.
I am not sure that I understood your question but I hope this helps.