Footbeds & Alignment
Footbeds are, in all actuality, only part of the "alignment" equation. Both Manus and Gandalf are headed down the right road. Manus mentions neutrality, Gandalf talks about center of knee mass. A boot that is properly aligned laterally, so to speak, will position you with the center of your knee mass over the center of the boot seam. There are any number of different opinions about flexed, un-flexed, etc... but generally speaking, with your weight just on the front of the boot you should get an acceptable measurement. It does sound like the fitter you worked with did a very good job of lifting your heels to drop your hips back. The tongue shim he gave you helps keep you upright, but is certainly much more of a band-aid solution for vertical alignment.
It sounds like the bootfitter you worked with measured you as knock-kneed or inside of the bootseam. If you are making a concerted effort to carve turns in a two-footed manner this is detrimental. Essentially, a knock-kneed stance makes it very to easy to roll the downhill ski onto edge, but limits how aggressive an angle you can achieve and also makes it hard to get your inside ski onto a similar angle (picture parallel shins). 10 or 15 years ago, this was widely accepted as the "way" to cant. Times, equipment, and technique have all changed dramatically since then. Additionally, your bootfitter should measure your two legs independently. He/she should tell you that you are X degrees inside or outside on a given leg. Once correction has been made (usually by using a cant strip) they should measure your other leg. It is amazing how many people I measure who have a noticeable leg length difference and this method reveals it. If correction is required for one or both of your legs then the fitter should keep playing with the amount of correction until you stand in that balanced stance on both feet while they are being corrected.
What a well-made footbed does in the alignment equation is more related towards eliminating problems with your feet (such as pronation or supination which are problems where you roll your feet to the inside or outside naturally) from the picture. The footbed will bring your foot to "neutral" so that you're standing with equal distribution. Gandalf mentioned varus and valgus, which are much more complicated, but equally important. See http://www.footmaxx.com/clinicians/five.html
for an explanation. Posting of a footbed will help eliminate these problems as well. I really think of a footbed as an interface between your foot which is, well, foot-shaped and contoured, and the flat bottom of your boot. One caveat: footbeds are only as good as the person making them, so do your homework.
Anyway, I've rambled long enough. I hope that helps.