It doesn't matter with your intended application. You've already found the proper wire to connect together. This is because you connected the two windings in series in the correct phase combination so that the voltages add. You will get the same effect if you connect Red and Blue. If, for example, you connect the Green and Blue wires together, you will get little or no voltage between the remaining two wires.
There's more than one way to get what you want. You can tie Green and Yellow together and use that as the common ground. Four diodes will give you + and - outputs with respect to the common ground. But the on-load outputs will be close to 12V, leaving little head room for buck (step-down) regulators.
There are regulators with dual outputs and you can use separate regulators for +ve and -ve. Many switching regulator ICs can be configured for either positive or negative outputs from a positive input. You could use a bridge rectifier to get 24V DC (higher with a light load) from the series connected secondary and use two regulators, one with +ve output and the other with -ve output. I'll leave it to those with more experience with switching regulators to recommend specific ICs.
One thing you should keep in mind is that switching regulators generally have poorer regulation and noise characteristics than linear types.