Hi Erik,
I assume you are talking about the Optimization library field in the Transition Settings - Prediction tab.
Charge state is supported there. This is all possible using + to denote charge, i.e. y6++ as you have used. We went a little cheap on the columns and the expressions, choosing to have "y6" be equivalent to "y6+", but because most peptides are charge 2, you should see PEPTIDER++ in the "Modified Sequence" column for most of them. Not sure if we would use just "PEPTIDER" for a singly charged peptide, but possibly.
I agree that it would be nice to have a way to switch to just showing the charge states (or adducts for small molecules) as separate columns. Perhaps we can add a checkbox for that at some point.
For the moment, however, you should be able to get what you are looking for once you understand the required format, which is pretty simple.
I have attached a screenshot of the Edit Optimization Library form when the CE Optimization tutorial is performed and its results are stored in an optimization library using Add > From Results. This is a great way to get examples of what Skyline expects. I will ask the developer responsible for the Optimization Library functionality to add this step to the CE Optimization tutorial.
Thanks for your feedback. Hope this covers what you were looking for.
--Brendan