Ok, I admit to never getting exactly how VBD works.
Since I have a few minutes while waiting for a long-running job at work, what the heck. I'm sure I won't say anything not already said in an article, but maybe I'll use an example that will help where another didn't.At it's simplest, what VBD is about how to compare the value of players at differing position. And what it says is that a player's value to a team depends more on how much he outscores others at his position (since they play against you), than it does the size of his season total.
That is, if RB1 outscores RB2 by 20 fantasy points, it doesn't matter if they scored 100 and 80... or 800 and 780. He's going to be just as valuable as a QB who outscore the other QB by 20, regardless of what they score.
Now that's easy to figure out in a two team league that starts 1 player at each position. Just subtract both QBs from one another, both RBs from one another, etc. The resulting number is a measure of his value to your team that can be compared from one player to another.
But what do you do in a 12 team league, where it's not just how your QB scores compared to a single other QB, but compared to 11 other? And what about when you start not 1 RB each, but 2? We have to decide what number to subtract away from the player. There is no right or wrong answer, and there are a lot of ways to go about deciding what number to use for each position. We call that number we're going to subtract the baseline. Most frequently people use the last guy who starts at the position (the 12th QB, the 24th RB, the 36th WR, etc).
Some average all the other players at his position and use that (with some modification perhaps to keep all the numers positive). And then some fudge the baseline further to account for other things... like the increased injury likelihood of RBs has some people (including Joe's Secret formula) fudging things to make RBs a little more valuable to reflect what he believes the true value should be on account of that. The idea in doing that is to make the list that is built of all players to be closer to what it should be.
But that is also in some ways a problem. One of the biggest problems with VBD is people misusing it because as you said, they aren't completely aware what it is telling them. It is a tool that tells you what the value of a given starter is vs the value of another starter regardless of position. But that isn't the same as telling you who you should pick.
The value is necessary input to the decision of who to pick. But there are other things to consider. The value of a backup isn't considered at all in VBD. Sometimes your RB3 will be more valuable to you than a starter. It doesn't take into account what will happen between this pick and the next. For instance, the best WR left on your board may have the higher VBD value than the best RB left on the board. But if you look ahead to your next pick and realize that there is little difference between the WR you can get next round, and the one now... but that there is a huge drop in RBs between now and then, you should take the RB even though he has a lower value.
I hope some of that is of use.