Baselines always get a little tricky... If in doubt, stick with Joe's Secret. It handles most leagues. In the beginning of DD (and VBD Spreadsheet), this was the only one available.
Some people are perpetual tweakers by nature... and wanted more control over the baselines. So we added the Worst Case Starter and the ability to create your own baselines.
The Worst Case Starter method is a standard one, so it is included with the DD. It is fairly easy for people to understand this one... but I'm not sure it is all that sound. Generally, if I'm going to use it... I use it as a starting point. For example, I'll enter the worst case starters into the "User Configurable by Position Rank" and then tweak the values up and down. For example, if you start 1QB, 2RB, and 3WR, etc. In a 12 team league, you would enter QB=12, RB=24, WR=36. Now if you wanted to increase the values of the RBs, you would increase this number, for example, RB=30. If you wanted to decrease the values of the QBs, then you would decrease this number, for example, QB=8.
One method that I've been playing around with this year (Yea, I'm a perpetual tweaker as well)... is setting the baselines by position rank based on how many players typically get drafted at that position. For example, if you start 1QB, 2RB, 3WR, 1TE, 1PK, and 1Def. and your league of 12 teams drafts 18 rounds. On average (you may have to look back at the past couple of years draft). You may find out that owners typically drafted 2QB, 5.5RB, 6.5WR, 1.5TE, 1PK, and 1.5Def (These numbers should be roughly equal to the number of rounds). In this case I mutiply each of the values by 12 (number of teams) and set the baselines as follows: QB=24, RB=66, WR=78, TE=18, PK=12, Def=18. With the limited number of samples that I've tried, the results look pretty good to me. I also like it because if you look at the VBD numbers... all of the draftable players have a positive number. If you start to draft a guy with a negative number... then that throws up a red flag... that you are drafting outside of the typical range.
There is also a discussion or two reqarding Baselines in the Shark Pool:
Discussion of Baselines