Im not sure, if I understand you correctly (okay, well I'm pretty sure I don't), but I think the problem rises from the difference between the pxl-commands and the plot-commands. The plot-command use the settings of the ViewWindow, so normaly something like x-axis from -6.3 to 6.3 an y-axis from -3.1 to 3.1, while pxl uses another coordinate system, top-left corner is (1,1) with y-axis turned down and x-axis turning right. The bottom right corner is on the legacy calcs (63,127) (note that first y and then x) and the prizm something different.

So a good approach to this problem is using a viewWindow, which makes converting to the pxl-coordinates relatively easy (ViewWindow 1,127,1,1,63,1), so PlotOn x,y is equivalent to Pxl-On 64-y,x or something similar. Also note that the plot commands override the X and Y variables.

(This is, because the "Plot "-Command without parameters can be used as an screeninput, it gives a cursor and retrieves the coordinates of the given point in X and Y. But PlotOn 13, 37 overrides these too).

I hope clearing the difference between these two help you sort out your problem.