If it’s depth of field you’re after then you need a smaller aperture as I’m sure you know. Problem is that with a flash a smaller aperture works directly against the power of the flash. You can offset this with a higher ISO. Try using aperture priority to get the right depth of field, use a DOF calculator if that helps, and then increase the ISO to get the exposure right.
If you’ve not already done so it mightn’t hurt to read the Strobist: Lighting 101 posts. With a little understanding of what’s going on it’s not hard to use your camera and strobe on full manual control to get good results. Don’t fear the manual settings! – http://strobist.blogspot.com.au/2006/03/lighting-101.html