>Run them both at the same time
>Will the apps take advantage of the dual core?
Start the task manager. In the "Precesses" tab right click on some process running, some of the last context menu items is "select affinity". Almost all processes will have cpu 0 and cpu 1 checked. You can force one of your exe runs on one cpu, the other on the second. But normally it's the job of the OS to balance cpu usage and it might get the idea, that your two exes will run best on seperate cores. I think you're better at leaving both cpu's checked, but just give it a try and see what's faster.
You might try
http://www.microsoft.com/technet/sysinternals/utilities/processexplorer.mspx and monitor cpu and core usage.
Bye, Olaf.