SignalSuite currently requires signal amplitudes to be specified relative to the full scale output level. The full scale level will be dependent on the selected audio output route (e.g. headphone output, or line-level output via the dock connector).
Once you know the full-scale output of your particular device, then you'll be able to output known voltages, as long as you perform the relevant conversion between full scale (FS) and volts (V).
I notice there is now a control to set output level. Is there a way to bypass this?
I'm not sure what control you're referring to, but none of the output level controls can be bypassed. You'll need to make sure they're properly set. The amplitude slider values are remembered when the app exits, but the slider in the Options screen is tied to the device volume, which can be altered with the physical volume buttons.