It's two separate windings. If you were building your supply anew, you could parallel the windings with a bridge, or for a little more performance, you could connect them in a CT arrangement with two diodes for full-wave rectification. However, as you apparently have already built it and it works fine--your 100mA stated output is within the specs for 1 winding--I certainly wouldn't go back and redo it. The unused winding is of no consequence.