I think you just treat DCIN as a signal to tell Edison that there's a DC power supply connected.
If you leave DCIN floating (I assume it's pulled down) and the voltage on Vsys is below 3.5V, it assumes that the battery attached to it is flat (3.5V with a small load is pretty much completely flat for a single LiPo cell) and aborts the boot sequence. Presumably if it doesn't rise from 2.5V to 3.5V in 10ms then that implies a substantial resistance in the supply wires, which is also a good reason to stop booting.
If you tie DCIN high (ie to Vsys) then you're telling it "this is a power supply". This means that Edison doesn't care if the supply appears to be "flat", and it doesn't impose a limitation on the supply rise time (power supplies with big output capacitors can take a while to reach the right voltage).
Having Vsys and DCIN separated by the power outputs is a bit annoying (hard to connect them together). I've ended up ignoring the Edison voltage outputs and putting my own 1.8V regulator elsewhere on the board.