Based on my experience I'm agreeing with most of what I read here. The four most valuable items are:

1) Use the term "transit" as a way of distinguishing between a stopover as defined in building and ticketing itineraries (which does not have any reference to duration of such a stopover) and a stopover as uniquely defined for SWU usage (which is less than 24 hours or, IIRC, the next possible continuing flight).

2) Get your record noted. The wording xpacific used is ideal.

3) Deal with Customer Service after the fact if the system consumes one too many SWUs.

4) Consider buying up to a fare which can be upgraded using miles.

What all the above does not help is the still stupid system (they supposedly fixed it three months ago) which reserves one too many SWUs, leaving you unable to use it to hold a seat on a later itinerary, or, if you don't have surplus SWUs, leaves you unable to even try to solve the situation using 1 through 3 above. You are forced to buy up to use miles, if you have enough of that commodity.