I did a roughly 8,500 mile trip a little over a year ago and kept things simple by giving the sleeping car attendant $20 when I got off the train and just left $5 per meal for dining car tips. I'm usually a generous tipper, though I have no problem with leaving $0 for poor service.

Most other people I dined with seemed to only leave a dollar or two at most, even for dinner. Amtrak staff aren't paid like a typical waiter/waitress, so the tips are more for appreciation and not as large a percentage as their income as the wait staff at your local cafe.