A few questions:
Is your 580EXII set to High Speed Sync (HSS)? That can cause a lower flash output.
Have you done a test with both flashes (flash on-camera versus flash off-camera) the same distance from your subject? Try this, shooting everything in Manual mode (both your camera and your 580) both times and see if you experience any light dropoff. Also, you will indeed see a reduction in flash output when it's positioned behind an umbrella.
Finally, when you say you may need to 'just turn the speedlites directly at the subject' does this mean you were using bounce flash before or are you bouncing the remote flash on the stand? When shooting through an umbrella it's advisable to have it aimed at your subjects (how much of an angle is up to you, but you definitely don't want to be bouncing a remote flash through an umbrella; that will indeed give you very little light). Bouncing your flash, on-camera, is intended to give the same look as if you shot the image with a remote flash that was aimed at the subject and shot through some kind of diffuser (softbox, umbrella, etc). If you don't have the ability to shoot with off-camera flashes, bounce by all means. If you are shooting with off-camera flashes, aim them at your subject (preferably through an umbrella or softbox).