Employees are eligible to be a member of Amtrak Guest Rewards, and participate under the same rules as any other passenger, with the following caveat: Minimum point earnings (including 100 points per segment minimum, and Acela city-pair bonuses) do not apply. It's just a straight 2 points per dollar.
Amtrak employees and eligible passriders can ride for free on corridor trains (except Acela and to/from Canada) by "flash passing" on the train. On long-distance trains, they are subject to a "red/white/blue" policy that is based on that train's history of selling out on that particular day in the past. Blue trains are free (no AGR ponts). White trains are sold at a 20% discount off the prevailing fare (rail fare & accommodation charge, if applicable), and if the train does not sell out, they get a refund of the 80% they did pay. Red trains are just sold at a 20% discount, with no refund. As I noted, standard AGR earnings apply (except for the minumum) to tickets that the employee pays for.
Sleeping cars are always sold at a "white" fare (so if that particular accommodation sells out on your train, you get no refund, but if it doesn't sell out, then you do). However, certain trains do offer the ability for employees to occupy space in the dorm car if the rooms are available within 24 hours of departure, and nobody traveling on company business has booked those rooms. That space is free (obviously, no AGR points), but does not include attendant service (find your own sheets, make your own bed) or free meals (pay for them in the diner on your own).
Off-peak Acelas are a flat $5 for business class or $30 for first class, if space is available within one hour of departure. That will earn you 10 (or 60) AGR points, so it's not exactly a points run candidate. There actually was a time when you could get the Acela city-pair credit (500/750 points) on an employee pass ticket, but that loophole was closed a while ago.
As of now, employees, spouses/domestic partners, and their dependent children (up to, I think, age 19, or up to age 25 if they are enrolled full time in school) are eligible for pass privileges under the same rules.
Employees traveling on company business, of course, travel for free, and therefore do not earn any AGR credit.
Freight railroad employees that have Amtrak pass benefits (basically, those that worked for the railroads before Amtrak was created) operate under a completely different set of rules that I am not familiar with.