Excerpt from Peter Riddle’s book, Greenberg’s Wiring Your Lionel Layout, 1991, p. 37:
Phasing is done by connecting a temporary wire from post A of one transformer to post A of the other. Then another temporary wire is connected to post U of one transformer only....The speed control handles are both set to the approximate midpoint, and the transformers are plugged into the wall socket. The free end of the wire from one post U is then touched to the other U post. If there is little or no sparking, the transformers are in phase, but if a strong spark occurs, the wall plug of one must be removed from the socket, rotated one half turn (180 degrees) and reinserted. There should now be little or no spark when the wire from one U post is touched to the other.
Addendum, courtesy Joe Pallone:
Just be sure to check that you are joining hot to hot and common to common (which is not necessarily A-A, U-U). Not all Lionel transformers use U for the common. Common on a ZW, KW & Z is post U, but on many single-throttle transformers (1033/1044, LW, RW and TW for instance) the U post is the hot.
Once the transformers are in phase, one good tip is to keep the transformers plugged into an outlet power strip so that you won’t have to unplug them from the wall, just turn the strip off; another is to insert each transformer plug into a three-pronged plug, which of course can go into a live outlet or an outlet power strip only one way, thus ensuring the transformers are always plugged in with the correct polarity.