I'm not completely certain I understand your question, but let me answer the question I think you are asking. Yes, all the transformers used on your layout should be in-phase - which means essentially two things - one that all the "base posts" are connected together (in some cases, that connection may be through the track). This sounds simple, and it is for simple layouts, but more complicated layouts its good to have some sort of circuit diagram so you can make sure all the base posts are connected together (obviously, if you had one transformer that simply supplied power to a bunch of isolated circuits, like lights, it won't matter - though I think as a matter of good practice and to avoid being confused, its still a good idea)
The other is that the 125VAC feeding the transformers is the same phase. Most 'vintage' transformers - such as the 12B - do not have 'polarized' plugs. Polarized means one prong is wider than the other, so it can only be plugged into the wall or a powerstrip in one orientation (the wider plug designates the neutral side of the AC circuit - the white wire in most cases inside a receptacle box). However, with a non-polarized plug, you can plug the cord in either orientation - which is what can cause a pair of transformers to be out of phase.
Checking the phasing is fairly straightforward. First, run a wire between the two base posts (transformers off is probably a good idea just to avoid an accidental short) If you have a volt-ohm meter, for the 12B, which has both a variable and fixed output posts, then I'd first check that both transformers have the same voltage reading (or close) on the fixed voltage output. Then connect the volt meter between the two fixed voltage terminals on the two transformers. If they are in-phase, the voltage difference between the two output terminals should be about zero (suppose the output of one transformer is 16 v and the other is 15.5 v, so in this case, you'd see a difference of about 0.5 v). If they aren't in phase, then the voltage difference will be the sum of the two output voltages - in this case 16 v + 15.5 v = 31.5 v (out of phase simply means that one transformer is at the top of the sine wave while the other is at the bottom, so you will be measuring that difference.
If you don't have a volt meter, you can do it with a light bulb, but you'll want to use the variable voltage terminals so if the transformers are out of phase, the combined voltage difference won't be larger than what the light bulb can handle. Here's a useful link the describes this in a bit more detail: http://www.kodiakjunction.com/...ks/TipsandTrick2.htm
Two really IMPORTANT things. First, its worth examining the powercords to the transformers to make sure the insulation hasn't cracked or opened up - aging power cords do that - especially near the plug or where the cord goes into the transformer. I've replaced power cords on several of my transformers, including a 12B. Second, once you have the transformers in phase, mark which prong of the plug goes into the wide slot of the receptacle (which should be the neutral side). I used a little stripe of white paint to remind me that that is the neutral side of the plug.
