For QB it's fine to calculate a player's value over a waiver wire replacement, since you may only roster one, but for other positions, I would suggest figuring out how many starting players will play that position, and calculate the difference between the player who's value you're trying to access, and the worst starting player at that position. Generally you'll replace an injured starting RB or WR with a player on your bench. Here are the steps I took:
1. Calculated each player's point value based on the league's scoring system.
2. Figured out the worst starter at each position. For instance, my league plays 2 rbs and a flex, so roughly 25 rbs will be starting. We play 3 wrs, so roughly 35 wrs will be starting. I didn't differentiate between flex rbs and flex wrs because I found that the #35 wr will be about the same production as the #25 rb.
3. Take each player's point total, and subtract the point total of the worst starter. In my league, Adrian Peterson was #1 while Ryan Matthews was #25.
4. Take an average auction price for the top player at a position, and the worst starter. AP has an average auction of about $59, while Ryan Matthews is about $11. Then divide the difference in point totals by the difference in cost. That will be how many points you should expect for each $1 spent. The number will be around 2.6.
5. Repeat step 4, but with WRs and QBs. my "points per dollar spent" for WRs was about 3, and it was about 2.8 for QBs. I averaged out these figures and used the number 2.78 as the number of points I could expect over a replacement for each $1 spent, and used that value for each position.
6. Take the point difference between the first player, and the worst player, and divide by 2.78 (or whatever number you came up with). This will tell you how much more that player is worth in auction compared to the worst player.
If you use an amount different than the standard $200, then just divide x by 200 and then multiply that number by the players value in a $200 league.
There might be a theoretical way to calculate each player's auction value without needing baseline values to start, but I didn't know how. I figured by starting with baselines and averaging out the value of a dollar in points, it would be fairly close. One thing to note is that if you have more than the normal roster spots, as my league does, (we play an extra receiver) then you need to devalue each player somewhat since you need to save some money for that last roster spot.
The conclusion I came to in my league was that receivers were undervalued and rbs overvalued, due to needing an extra wr in the lineup, and the fact that we got .5ppr.