You should be able to do what you describe. You will need two overlapping coordinate system, each initially scaled. Charts with two or more coordinate systems are discussed in our FAQ http://www.quinn-curtis.com/QCChart2DFAQs.htm. You will need a separate RTScrollFrame for each coordinate system.
The RTScrollFrame does not have to process purely time increasing (monotonic) data. They can process non-monotonic data in a XY graph, with autoscaling, similar to our RTXYPlot example. You do have to specify a y-scaling mode in the RTScrollFrame constructor, and a TimeStampMode set to RT_NOT_MONOTONIC_X_MODE.
RTScrollFrame scrollFrame = new RTScrollFrame(this, inputChannel1, pTransform1, ChartObj.RT_AUTOSCALE_X_MINMAX, ChartObj.RT_AUTOSCALE_Y_MINMAX);
scrollFrame.TimeStampMode = ChartObj.RT_NOT_MONOTONIC_X_MODE;
If you would like us to write a custom example program to your specification, let us know and we can give you a quote.