Sorry, we didn't get back to you on this one. I hope you have found that the answer to these questions is, yes.
I believe all of the places Skyline asks for peptides, it will also accept modified peptide sequences, like pasting directly into Skyline, Edit > Insert > Peptides or Transition List, and Refine > Accept Peptides. Some also accept charge state expressions on the end of the peptide sequence for specifying the exact peptide precursor.
Here also is another support request describing the various formats Skyline accepts:
Hope this is helpful, even if you managed to find a solution that worked for you already.