In the Big Ten, Horizon, and MidAmerica leagues we tell the catchers and pitchers in the first inning when there are "two more". In the second I tell them "throw the 5th one down". And yes, I count anyway to make sure and remind them if they abuse the number of warmups.
As for the PU between innings - I was taught at umpire school to stand on the side of the team coming off the field. That avoids that batter you just rang up on that borderline pitch running past you and making a comment he probably shouldn't. If he has to yell that comment because you're on the other side of the field, it's easier to deal with.
JJ
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