All goods questions, Howard. I'll try to give you some good answers! ?
Before the game, If I see any lines incorrectly marked I will bring it to the attention of the coaches. Then we either fix it, if time allows and the equipment is there to do it right, or wipe out the line altogether if it can't be fixed. Either one of those will usually solve any problems with a small area like the batter's box.
I've had cases where the entire foul lines were marked wrong, either coming from the front corner of the plate, instead of the point, extending to the inside of the bags, instead of the outside, or just so darn crooked they look like a West Virginia highway! If there is no time to re-do them, I'll tell the coaches that I'm ignoring the marked lines and using my own judgment to line up fair/foul balls.
My pre-game plate conferences are pretty much by-the-book: An introduction of myself and my partner to the coaches; Give me your line-ups and we'll review them real quick before they become "official"; A quick rundown of the ground rules; A reminder to the coaches about their players being properly equipped; Any questions?; Have a good game!
I don't go into any "what-ifs", mini-rule clinics, explanations on my judgment or special warnings before the game. The exception might be if, at the end of the meeting, a coach has a question about a certain rule or situation. Then I will quickly, and gladly, answer his question.
The rules are what they are, my judgment is what it is, and if they're wondering how I'll handle any special situations they'll find out in about two minutes once the game gets started!