Hi Chris,
Great question.
I would use the Output | Save User Specified Format Output menu and select the Output Analytical Errors in Relative Percents checkbox. Most plotting programs (e.g., Grapher) will allow one to select error bars from a data column in relative percent.
The reason to use the analytical errors calculation is because the program utilizes both the unknown and standard peak and background intensities for properly propagated errors due to counting statistics. And this can be calculated for a single datum.
Of course there are probably additional random errors but those are more difficult to quantify. But assuming that one has acquired replicate data and that the composition in question is homogeneous, one can simply use the standard deviations (also available from the Save User Specified Format Output menu) for the purposes of errors bars.
This latter method has the advantage of including all sources of imprecision in the error bars.
But make sure you have the most recent version of the software (10.1.x) which can be downloaded here:
http://www.probesoftware.com/Update.htmjohn