Q: how to use Disk Utility to format my disk as a single Mac OS Extended (journaled) volume

This got asked many times since 2007. Use anything you know how to and make a backup, erase the primary boot drive and restore.... usually cloning software. If you can't then you aren't really prepared for when there is a disaster and you need to is how I see it.

You can try shrinking the primary partition and see if the system can move files, consolidate free space, so you end up with the proper contiguous free space needed. But you shouldn't if you don't have backups, regardless of error message or not, before making changes.

If you really have not upgraded to Lion or above, I would. That way you have a recovery partition.

If you are using Mountain Lion great you have the latest, and the most current Windows drivers. And you can boot from and use Time Machine and Recovery Mode.

Maybe your program does not need to be run natively in Windows and would do just as well using Windows under Mac OS X, in a virtual machine environment instead and less trouble.

I suggest you actually open Disk UItility. Go to Help menu and "Restore" as well as look at how to use the RESTORE tab in Disk Utilty.