A fare "bucket" is a certain number of seats or rooms sold at a given fare.
Amtrak publishes four coach fares, five roomette fares, and five bedroom fares for each given city pair. A certain number of seats, roomettes, and bedrooms are placed in each fare bucket.
Seats, roomettes, and bedrooms start selling at the lowest published fare. When all of those seats or rooms are gone in a given fare bucket, the system starts selling rooms at the next higher bucket, and so on until the highest bucket is reached and then the given item (seat, roomette, or bedroom) is sold out.
Let's put together some sample fare buckets for sample city pair on a sample train with 210 coach seats, 42 roomettes, and 15 bedrooms (this particular train would likely have 3 Superliner coach cars and 3 Superliner sleeper cars, and I'm ignoring the family and accessible bedrooms in this sample):
COACH (210 seats available):
$150 (seats 1-75)
$200 (seats 76-125)
$250 (seats 126-175)
$300 (seats 176-210)
ROOMETTE (42 rooms available):
$300 (rooms 1-10)
$375 (rooms 11-18)
$450 (rooms 19-28)
$525 (rooms 29-38)
$600 (rooms 39-42)
BEDROOM (15 rooms available):
$400 (rooms 1-3)
$600 (rooms 4-6)
$800 (rooms 7-9)
$1000 (rooms 10-13)
$1200 (rooms 14-15)
In other words, if 20 out of 210 coach seats on a train are booked, then the next two (the ones you want to book) will still be available at the lowest fare bucket ($150). If 40 out of 42 roomettes are booked, the next one will be sold at the highest price--the highest bucket ($600). And if 7 out of the 15 of the bedrooms are empty, then the next one will be sold for one of the middle buckets ($800). This is how bucket pricing works.
Off-topic side-note: Airlines operate on a similar principle, but they play all kinds of weird games with their fare buckets, such as placing certain advance purchase restrictions on some [e.g. 7, 14, and 21-day APEX] fares, requiring round trips for certain low fares, publishing low fares with just a couple of seats in that fare bucket so they can advertise the low fares, publishing new fares and removing old ones sometimes hourly, lowering the price or introducing a new lower fare bucket to try to drum up business, etc. Amtrak has a very simple system in comparison, since the same four (and five for sleeper) buckets are always the same price and are sold directly relative to how many other seats have already been booked on a given train. That's why we always say around here to book early, since the fares can only go up! (Airlines often hold their prices at a medium level and then start to drop fares and get into fare wars 3-4 months out. Not so with Amtrak.)
Anyway, let's say you and your spouse book one of those high-bucket roomettes at $600 and board the train. You wanted a bedroom, but it was being sold for $200 more than the roomette. Now, if there is space available, you can upgrade on-board the train to a better accommodation. One of the benefits of an on-board upgrade is that, no matter what (even if there is only one room left), they are sold at the lowest bucket, and you only pay the difference between what you paid and the low-bucket price of that room. So if you get on and ask the conductor to upgrade from a roomette to a bedroom, he will sell it to you at the lowest bucket. If you paid the highest bucket for a roomette (in our hypothetical, $600), the low bucket for the bedroom (let's say it's $400) will likely actually be less than you paid for the roomette. In this case, although it would be nice if the conductor actually gave you back money, instead you will pay the minimum $50 upgrade and then be moved into a bedroom. Still, $650 is a better deal than the $800 it would have cost to book the bedroom at the middle-bucket price initially! (The same principle applies to upgrades from coach to roomettes and/or bedrooms, although I doubt even highest-bucket coach is ever more expensive than a low-bucket sleeper.)
On-board upgrades only make sense when the accommodations are not selling at the lowest fare bucket. They are never cheaper than this, so if you are booking your trip and find a roomette or bedroom at low bucket, go ahead and book it then--upgrading on board will not save you any money.
Now, how do you tell what the low bucket price is? That's a good question. An old trick is to do a test booking for 325 days from today. Amtrak starts selling tickets for travel 330 days out, so if you book for 325 days out, you stand a good chance of finding seats and rooms at the lowest bucket. Make a note of that price and then do a test booking for your preferred travel dates--if it's the same, then you're buying the seat/roomette/bedroom at the lowest bucket! If it's more, then, well, you're not--you can play around with your dates and try to find a train still selling at low bucket, or, if you're looking for a sleeper, you can book coach now and attempt an on-board upgrade.
I might have also heard rumors that certain bucket prices can be found in the Amtrak timetable, but I can't confirm that rumor. AlanB might, though (I think he's the one who posted something about that awhile back.)
Another confusing sidenote: I'm also deliberately ignoring the railfare component of the accommodation, since the above principles work fine ignoring it, but here's how that works: when you buy a sleeper, you are charged for two things: the railfare and the accommodation charge. The railfare is always exactly equal to the price of a coach seat at the lowest bucket. This works in your favor in the event that coach seats are selling for a high bucket--let's say 290 out of 300 seats are booked and they're going for $300--but roomettes are pretty empty--let's say 2 out of 30 are sold and they're going for an accommodation charge of $300. The final price of the roomette for two people will be $600, or the $300 accommodation charge plus the $150 low-bucket coach fare per person times two, since that is the base railfare, even though coach seats are selling at twice that. The reason I say this works in your favor is that most people will click the "View Upgrade Options" button and see that the roomette is going for $300 and automatically assume that it's $300 on top of the $600 coach fare (for two people) for a total of $900. However, now you know that upgrading to the roomette will cause the railfare component to drop from $600 to $300. And if two coach seats were selling for $600 and it cost the same $600 to book two people into a roomette, which would you choose? I thought so!
Also, the railfare is the component that qualifies for the AAA, NARP, SA, VA, etc. discount. The accommodation charge is not discounted by these programs.
I think this is my most comprehensive post about the bucket system I've ever done. I should save it for future reference...after rewriting it for readability, of course! Anyone have any corrections or suggestions?