I've plotted data sets with different y values, but they used the same array of x values. I'm not sure that you can use two sets of x values.

I have the O'Reilly book Programming Web Graphics with Perl & GNU Software. It is rather out of date because the graphing section it uses GIFgraph, which is deprecated, but there are few differences between GIFgraph and GD::Graph.

Here's what the book says for datasets:
"The data for the graph must be in a very particular form before you plot the graph. It must be assigned to an array, where the first element of the array is an anonymous list of the x axis values, and any subsequent elements are different data sets to be plotted against the y axis. A sample data array would looke like this:

@data = ( # First the time span
[ qw(1992 1993 1994 1995 1996 1997 1998) ],

# data set 1 = 1000s of people in Peoria
[ 5, 10, 8, 13, 16, 24, 32],

# data set 2 = 1000s of people in Santa Fe 
[6.5, 9.2, 14.2, 12.8, 22, 31.7, 2] );"
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GD::Graph::mixed is for graphing multiple data sets and making one points, one lines, etc. When I've used that though I've just had one x value array.