This is more of a guess than anything else, only the Madden team could really answer this for you, but from what I've seen, in Player Scheme WR1 will refer to who is listed first on your "roster" not your depth chart, because the ratings on your roster are listed by overall so this is who the cpu says is your best WR. Your 2nd best wr as deemed by the cpu (roster) would be the WR2 and so on. But to be brutally honest, I'm not even sure that the function works as intended and I think only the scheme WR1 is applicable at any time. Same with CB and HB. Although whether there even
is a HB2 is based on the team you are coaching, so I think it is all tied together in that respect and not really with the
2 options in player schemes.
I guess in other words I'm trying to say it is broke when there is more than 1 scheme per position.
not gospel by any means though and maybe someone has actually play-tested it and will answer...