I am not sure I understand your question.
One thing that Skyline is not good at is dealing with peptides that could not be found in the sample. Skyline always tries to choose the best peak, and so, if the peptide could not be found in the sample then Skyline ends up telling you about some peak areas that Skyline found somewhere else.
Unfortunately, we do not have a good answer for what to do about this yet. We do sometimes point people to the advanced peak picking tutorial, but that probably won't help in your case:
It sounds like you are asking about something else, but I do not understand what you are asking.
Could 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.
If that .zip file is less than 50MB you can attach it to this support request. You can upload larger files here:
It might also be helpful if you could send us a screenshot of what you are asking about.
In terms of adding modifications to the document, there really is no easier way than doing "Settings > Peptide Settings > Modifications > Edit List > Add". The idea is that you would define all of the modifications that you need, check the checkbox next to all of those modifications in the list boxes at "Settings > Peptide Settings > Modifications" and then save your blank document. Then, whenever you want to create a new document you would copy that blank document and start from there.
If you needed to define a really large number of modifications, you could theoretically use a text editor on the ".sky" file. The Skyline document is an XML file and the syntax for how modifications are declared in the .sky file is pretty straightforward.