The past few weeks I've been reading a lot about flash (Light, Science, & Magic; Speedliters Handbook), and watching lots of videos (Mark Wallace, Scott Kelby, etc), so I think I have this correct. Wilt will hopefully be along and set me straight if I'm not. 
The exposure meter is simply telling you what the exposure should be to capture the ambient light correctly. It doesn't know squat about the exposure with the flash, until the preflash (aka Ninja flash) fires, and it then calculates an exposure based on the preflash. The camera then decides what settings it and the flash needs, and tells the flash what to do. This is the e-ttl part. You may or may not like what the camera decided was best.
So, let's say you didn't, and you want more ambient light. You'll slow your shutter down. Just because the fastest sync speed is 1/250, doesn't mean you can't go slower (or fast if your flash supports HSS). Going slower will increase the amount of ambient light that gets to the sensor.
"But I can do that with aperture" you say. Yes, but you're choosing your aperture primarily for the DOF you want, not for additional light. Changing your aperture will alter your DOF, and change the overall look of your image.
Changing shutter or aperture settings when using a flash and e-ttl, will only have an effect on your background (the ambient lit areas). When you lower your shutter, the camera will stop down the aperture, and vice-verse. Stop down your aperture, it'll slow down the shutter speed, and vice-verse. In any of those cases, the e-ttl will still expose the subject the same (or pretty close), but your DOF will noticeably change. So when you want more ambient, you need to slow down the shutter to achieve that without changing your DOF.
How am I doing so far, Wilt?
As for moving your lighting, that is akin to increasing or reducing the power output of the flash. Move a softbox 6", and you may have changed the flash exposure by 1/3 stop, or possibly more. The camera will then change it's chosen settings based on that 1/3 stop change, again altering only what's happening to the ambient, not the subject, because the camera's goal is to expose the subject correctly. It will expose for the light coming back to it off the scene (subject) from the Ninja flash. Your camera doesn't care about the background, it just wants the scene to be 18% grey when all the colors in the scene are mixed together.
Typically, you'll want to expose for the desired ambient affect, then adjust accordingly for the final shot. My procedure is to choose my DOF (aperture), and then pick my shutter speed for the ambient light levels I want, then bring the flash in and either +/-EC, or +/-FEC as needed. A light meter would help, but....
So, in answer to your question, no, I don't use the meter in my camera, but I also shoot pretty much in either full manual or AV.