Forward transition on the 539s was automatic but to make backwards transition you had to close and reopen the throttle. You didn't have to move the handle for backwards transition, unless you wanted to keep the unit in a particular connection, I.E going up a stiff grade and you wanted to hold in series. Personal experience, and also in TP-105 and TP-107.
Britt is correct, the single unit (non-MU) locomotives had a seven position reverser. Off was in the center, one position forward (or reverse) gave you series, the middle position forward (or aft) set the unit up for series-parallel, the third, full forward (or reverse) position allowed reduced field operation.
A good analogy would be a three speed automatic transmission in a car: P-R-N-D-2-L. Almost all of the time we go right to Drive, and the transmission automatically shifts up through L and 2 to the third gear, D. But on a hill, or with a trailer, we may want to stay in 2 or even L. The transmission goes to that gear and won't advance to the next one.
Kicking cars, as mentioned in the Alco TPs, (and also in EMD manuals), is when you want to stay with the series connection, and "forstall" (again, borrowing the term from EMD) transition. But for road operation, crank the thing all the way to the end and open the throttle.
The MU units had a three position reverse handle: F-Off-R. A seperate push-pull switch on the control stand was used for "series hold", which kept the unit or entire consist in series. There was no way to allow series-parallel operation, but to disable reduced field.
If anyone comes up with any more on this transition myth, please post it here. But every 539 I've seen, and every manual or schematic I've collected and studied show that transition was automatic forward, and manual backwards.