You can run both with a little work.
First, you will have to see if the cable to the 40gig drive has a second connector available. If not, then you will have to replace it with one that does.
Second, you will have to see if you can physically mount the second drive in the case within reach of the second connector on the HD cable. Also you will have to find an available power connector for the second HD.
Third, configure the 40gig drive as master using the jumper next to the data connector on the HD.
Fourth, configure the second drive as slave using it's jumper.
Fifth, connect the power, the second data connector to the second HD.
Boot the PC.
Good luck!