On Jetnet, there are two ways to check-in. First, there is an app called, Jetnet Check-in, (isn't that original and cute?

). You can check-in for flights today or tomorrow if within 24 hours of scheduled departure. You select day of travel (today or tomorrow and it displays day of week and date for each). You then enter Departure location and flight number. If you then hit Continue, it takes you to the next page which is a confirmation of your information, and gives you the opportunity to put yourself on the upgrade list for First Class (or when you make the reservation, you can list for F/C which may or may not mean that you get a F/C seat. There are those people known as revenue passengers that keep getting in the way of my upgrades.
if you don't remember the flight number, you can go to "non-rev travel planner" app) which will display all of your non-rev listings that are active. Click on the appropriate pnr id then select "checkin" from a drop-down list. That then takes you to the jetnet checkin app with the flight and date info, and gives you the chance to request upgrade to F/C.
At the time you checkin, if the flight is not close to full, the system will go ahead and assign you a seat in coach and you can printout your boarding pass at home (I recommend this. That way there is less chance that another passenger will get assigned the same seat).
The jetnet checkin app is closely connected to the computer clock. If you try to checkin more than 24 hours prior to scheduled departure you will get an error message. However, it does not wipeout the information; so, when it gets close to the checkin time, you can just sit there hitting the continue until it displays a boarding pass or an error message. If the flight is close to full, you will get the Priority Verification display (which gets you through TSA security). The Priority Verification looks like a boarding pass except it just doesn't have an assigned seat number on it.
Justme: When you get checked in and the Boarding Pass/Priority Verification card is displayed, there is a link on that display to check the Standby List, it will show you the real time position and 1st 3 letters of the non-rev names and revenue upgrade requests. For instance I always show as Upgrade Pas and my check-in time; so, there is no question of whose is first, second, or third, etc on the standby list. Also, IIRC, it also shows who is D1, D2, D3 (non-rev codes, D1 being highest priority), and they are listed in that order.
Warning: Don't even THINK of checking in as a D2, seeing that you are way down the list; so, you decide to cancel your listing then relist as a D2 and checkin again. The computer tracks this, and it is a violation of travel policy that can cause you to lose ALL travel benefits.
P.S. Bogey you are correct. if you check in first as a D2, you will be ahead of all other D2s originating on this flight, but someone checking in as a D1 would list ahead of you. Also, a D2 who was listed for an earlier flight and wasn't able to board (not showing up at the gate doesn't count) will roll over to your flight ahead of you, but behind D1s.
Listing as a D1 must be used sparingly because employees are given 4 D1s per calendar year. The computer does not stop you from listing and traveling as a D1 a fifth or more times; however, it does spit out a report of you violating the travel policy which can cause loss of all travel privileges. Fortunately, there is a travel history app on Jetnet Travel that shows you the current year's travel history for you and all of the people on your "buddy pass" list. It is your responsibility to make sure you don't exceed 4 D1 travel events per year.
Of course, all of this post assumes that the current AA policy will survive intact in every way. There is no preference given to employees commuting to work. The company's position is you choose to live somewhere other than your base. That does not give you a leg up on employees traveling on vacation. Exception: Pilots who are commuting to work and the flight is full and there is more than one pilot listing for the cockpit jumpseat(s) can call their Crew Scheduler and get themselves changed to an A (traveling on company business) classification which puts them ahead of everyone other than previously listed A category employees--even revenue passengers. (I think there may be a limit to the number of times an individual pilot can do this, but I don't know for sure.)
One other caveat: On-line check-in may not be used within 1 hour of scheduled departure. You have to check-in at the ticket counter or gate. Exception: say you are listing for PHL-CLT-PHX. For CLT purposes you go on the standby list as a D2T (through passengers) the moment you board your flight at PHL. Through passenger non-revs go on the list ahead of originating D2s (or D1s as the case may be). One thing the company does not want to do is strand employees at an airport other than their home or destination airport. If it's your home airport, you can always go home and try again tomorrow. (If you commute to that airport, then you want to be sure that your flight into your base and your flight out of that base are on the same PNR; then you will be a D1(D2)
T on that outbound flight.
And, for those of you with devious minds (like me) who might think "Well, I'll just book a turn PHL-PIT-PHL-CLT-PHX instead." NO, you can't stick an incidental turn at the beginning of a listing to make yourself a through passenger at your normally originating airport. That is another travel-benefits-losing violation. (I think it came about due to the sheer volume of super short flights out of DFW, such as DFW-AUS, DFW-LBB, DFW-SAT, DFW-OKC, etc.)