how multiply pronunciations per word affect the alignment

[ita...@gmail.com]

hi everybody 

When a single word , has 2 or more  pronunciations in the lexicon , than which one is placed during the alignment ?  

By alignment I mean the "tagging"  or labeling the phoneme , or tri-phone  per each frame  ,which than is used for the NN supervised training.

So if a word has multiply pronunciation  , does it splits the alignment to multiply "labels" or chose the most likely pronunciation  and use it to label  the frames ? 

thanks