I am not sure that I understand your questions.
The Average Mass Error PPM value that you can see in the Document Grid or in the Results Grid is calculating by taking the weighted averages of the mass errors of the transitions under that precursor. The mass errors are weighted by the transition peak area. If a transition has been marked as "non-quantitative" (you can right-click on a transition in the Targets tree to mark it as non-quantitative) then the transition will be excluded from the precursor's Average Mass Error PPM calculation.
I am not sure exactly what you mean about displaying or selecting only 3 of the 5 ions that you imported. When Skyline calculates the average mass error PPM for a particular precursor, that calculation is not going to be affected by what is selected in the Targets tree.
If you would like to learn more about the Document Grid and the Results Grid, you should take a look at the Custom Reports tutorial:
In the years since this question was first posted, we have added several new mass-error-related graphs to Skyline. You can see these graphs by using the menu items located at:
View > Mass Errors
I am not very familiar with exactly what you can see in those graphs, but one of them might have the information that you are looking for.