I don't have an ST-E2 so cannot confirm for sure. However, I don't use E-TTL in the way you're suggesting. I use it when speed is essential and there's no time for messing about, such as a social situation when I can just plant a couple of Speedlites around the room bouncing off the ceiling for fill-in and just hit the button knowing I'll be there or thereabouts with the first shot. It's fantastic for that.
The only other time I'd use E-TTL would be in a trickly situation when I cannot get easy access to control the remote guns, because they're up a tree or inside a car or something. Another situation where E-TTL makes very difficult things easy.
For the studio situation you're describing with plenty of easy set up time, not only is manual control easy but I would say preferable in that once it's set, the exposure is locked. Furthermore, you also know what power each gun is firing at and in that situation I would use that knowledge to moderate the power output down to a level where I was getting fast recycle times. Shooting portraits with a five second recyle time is completely hopeless and even if one of your guns is firing at that slow rate and the others are much quicker, you're stuck with the longer time. You'll find yourself shooting before they're ready and one or more won't fire or will go off at less than full charge - flippin useless.
If you're concerned about exposure metering using manual, well yes that's a problem and a flash meter makes life much easier. However, you can do it without by reading the histogram and blinkies. I would do it like this:
Set up the background lights and make sure the light is as even as possible. If you have two identical guns set at an identical distance and angle, you can't go wrong. Adjust the power/ISO/aperture so that a shot of just the background alone gets the blinkies flashing (over exposure warning), but only just.
Now switch the background lights off and without changing the camera settings adjust the power of the front light until you get perfect exposure. Your ratios should now be set. Now switch everything on and see what it looks like. You'll probably get over exposure in a normal room as the background will have some influence on the overall scene, so moderate that with f/number or ISO.
That should get you pretty close to where you need to be. Depending on how it looks on the LCD/histogram/blinkies, play with the settings slightly to get it just right. Guard against giving the background too much exposure as it's easy to do and might well look good at first glance, but when you get to check the finished result the outline of the subject, especially hair, will be bleached and eaten away. If you have a flash meter, aim for half a stop over-exposure on the background, one stop max.
Of course, you can do the exposure thing by working the other way around and set the front light first. Doesn't really matter, depends on the settings you want to use and where you've got most latitude for adjustment. It only takes a few minutes to do this when you're familar with the routine, but once you have a basic set up and have noted all the distances, angles and power outputs, you can replicate it any time. Bear in mind that flash is very sensitive to distance and in a studio situation just a few inches makes a difference, and a foot out can put you in trouble.
HTH
Would obviously work just as well with a 580EX flash on the end too. 