Got it working. This required a visit to Atari Age to understand what was going on.
There are some protections in A800 disks that lr-Atari800 can't get around but Altarri can. This was one of them, hence the odd error message. The emulator reads the disk, but it's not jumping over the sector of copy protection.
I was graciously given a "newer" version of CA that had the protections removed.
The underlying Linux operating system that RetroPie runs on top of is intrinsically multiuser.
You only need a free TeleTYpe program (I recomment putty for Windows) to gain access from your laptop in the same way as WinSCP does to move files.
Username pi - Password raspberry
The pi user does NOT have administrator rights, but the 'run as super user' keyword "sudo" can be used in front of any commands that needs them (no admin password required).
Make the terminal window as big as you need and use the nano editor to change configurations.
@grand_national to exit Atari 800 standalone emulator you have to use the keyboard (F9). F1 enters the configuration. Only retroarch emulators and a couple of standalone emulators like amiberry and mupen64 support exiting with the select+start combination. But the standalone Atari 800 emulator is a lot more functional than the libretro core.
Ok I just did one more test and I downloaded the Atari800 core from the retropie setup and it does have perfect sound quality (audio coming from my left speaker only, though), and it uses the same BIOs files than the lr-atari800 core. Is this normal? I want to use the lr-atari800 because of the keyboard being mapped to the joypad, or maybe if it is a way to get into the Retroarch menu in Atari800, and the set up my gamepad being Atari Joystick?
If the game starts automatically then everything is OK, otherwise one of these 2 conditions may occur:
1. Black screen
2a. Atari logo and "Copyright 19 Atari" text
2b. Crash screen: "!!! The Atari computer has crashed !!!" and a series of options
If condition 1 occurs, you must do this:
a. Press F5 if you have the keyboard inserted, or X button on the joypad
The system will perform a "warm reset" and at this point you will arrive at condition 2.
If you have the keyboard connected: press ALT + C,
If you only have the joypad (not recommended, because many games require the keyboard), click A with the joypad on "Menu" and in the next menu click A with the joypad on "Cartridge Managment"
Select "Cartridge: none" and press the enter key (or A with the joypad) (there may already be the name of the rom instead of "none", but it does not matter)
Now you should see the directory (atari800) with all the roms, and the rom you have chosen in the emulation station menu already selected
Press the enter key (or A with the jpypad) on that same rom
A new menu will open: "Select Cartridge Type"
Select "Standard XX KB Cartridge" (where XX may vary with 8, 16, 32 or 64 depending on the selected rom) and press the enter key (or A with the joypad)
Then you will return to the menu: "Cartridge Management", press ESC and again ESC (or X and again X with the joypad)
The game will be launched!
* it may happen that the menu: "Select Cartridge Type" does not appear. No fear, just press ESC and again ESC (or X and again X with the jpypad) to launch the game.
The stand-alone Atari800 emulator, not the Retroarch lr-atari800, you can goto the menu (F1), then "Display Settings", then scroll down to "Color preset" and select "Vibrant". That fixed the washed-out look, for me. There is also a manual "Saturation" setting, under the color preset, so you can further increase the saturation, if required. Mine is set to 0.28.
Fortunately, in the last possible attempt before having to type lines like THAT, I got it all working...
Very nice! Glad to hear everything's working now. Something to keep in mind for future endeavors is that no one actually types command lines like the ones listed above, as there would be too much margin for error. For situations like that, a quick copy and paste into a remote ssh session will save finger cramping and your sanity.
It should let you edit it now that some time has passed. If not, I'll delete it and you can post your revision below. In any event, thanks for posting your solution. I don't currently have any games in mind that this would apply to, but I'm sure I'll run across some eventually and I'll give this a shot.