You are correct, dark wing, the WR "custom depth chart" doesn't work the same way that the ones do for TE, RB, FB, QB, and BTE.
The WR custom depth chart spots always correspond to the number of a WR in a play. So, Big I formation would only have a WR1 in it. If you have one WR in the WR1 depth chart spot, he will ALWAYS be in that spot, nothing you can do about it.
In all the formations that have 2 WRs on the field, they will be the WR1 and WR2, respectively, and so forth.
What you CAN do is just to mix putting WRs in the generic WR depth chart slot, and then leave one or more (or all) of the WR1 to WR5 slots empty. Then, if you have a possession WR that you want to put special routes in as a WR3 (for plays that feature at least 3 WRs, remember, so you have to look at the formation), you could put that WR in as the only dot in the WR3 custom slot, and put all your speedy WRs in the WR slot, where they will be pulled from as needed, based on your energy settings.
Hope that made things less clear for you.

One thing I don't know for sure is what order things are pulled in. For example, if you had a WR in the WR3 slot but also in the generic WR slot, and you ran a play with 4 WRs in it, could your WR3 dot get pulled first into one of the other slots, based on energy settings, and then one of your other WRs would be pulled in to the WR3 slot since it would now be empty? Or does the pulling start by looking at the WR1-5 slots? And, if so, does it go 1-5, or 5-1, or some sort of random unpredictable way?
