It is certainly a pain in the butt! Toll-by-plate is probably the easiest to manage although I fear receiving 20 letters/billings as each area would have their own piggy bank.
Really confounding for me now is having both a Florida SunPass sticker and a Maryland EZ-Pass velcro. I bought the SunPass sticker as my parents were living in Central Florida and I was having to use the turnpike or roads around Orlando (which are a maze of different toll systems including short segments of EZ-Pass but also SunPass and some other -Pass). So now I need to be sure to remove the EZ-Pass (and not forget to attach it later) plus shield it from being double-billed. At some point, always in the undefined future, both SunPass and EZ-Pass will be interchangeable throughout their respective regions... but who knows when and how that information will be communicated.