I do not think that Skyline will be able to permute the set of variable modifications on the crosslinked peptides and add them to the document the way that Skyline does with ordinary peptides.
The easiest way to insert a large number of crosslinked peptides is to use the "Edit > Insert > Peptides" menu item.
There is a description of how to specify a crosslinked peptide sequence using the "-[crosslinkername@position1,position2]" on pages 9 and 10 of the "CrosslinkingInSkyline.pdf" file here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=Crosslinking
The column "Peptide Modified Sequence Full Names" in the Document Grid will show you what the modified sequence for the peptides in your document which might be helpful for you when you need to compose the crosslinked sequences for the peptides that are missing from your document.
-- Nick