do you tip with the bill?

depends if youre paying with card or cash. If you're paying with a card you tip with the bill, but if youre tipping with cash you leave it at the table generally.

And if you paid for your food and your change should be less than a dollar, do the waiters just take it as tip? (Let's say your bill is $19.71 and you give a $20, will the waiter just keep the 29 cents as a tip?)

yeah, and theyre mad at you for only tipping 29 cents

it's a whole crisis when you pay $20 for a $19.50 meal at iHop and then wait 15 mins before getting seriously concerned and confused

is this really..? sounds like a super avoidable situation where you're the one being dumb about it. a 15-20% tip is expected, and if they think you're only tipping 29 cents AND THEN YOU ASK FOR THE 29 CENTS BACK..good lord dude. dick move