Not much setup is required, but you may optionally put a system bios as boot0.rom in your Atari7800 ROMs folder to use before loading a game. It may increase compatibility in some rare cases if used. This core does rely on properly configured Atari7800 headers as detailed here. Using Trebors 7800 ROM PROPack is recommended as this is a reliable source of correctly headered ROMs.
Most 2600 games are supported including most bankswitching schemes, with a few exceptions. ARM based mappers, such as DPC+ require a 70mhz ARM cpu, which would be either very difficult, or impossible, to have run properly on the cyclone V that MiSTer FPGA uses. To make the experience better, an Out of Order screen will be shown when one of these games using modern hardware is loaded. A few more eccentric peripherals are also not supported simply due to lack of any practical purpose, but anyone is welcome to add them someday if there's some need. This includes the Compumate and the Gameline peripherals. That said, the following bankswitchings are supported: F8, F6, FE, E0, 3F, F4, P2, FA, CV, 2K, UA, E7, F0, 32, AR, 3E, SB, WD (8k dump), and EF. Bankswitching will now auto-detect the correct type, and does not require special extensions.
The paddle peripheral is mostly used in 2600 games and has special handling surrounding it because of its unusual 2-paddles-per-port configuration. Three types of inputs are supported for paddles: analog sticks, mice, and mr. spinner compatible joystick adapters. It's important to note that PADDLES HAVE A DEDICATED FIRE BUTTON in this core, and it must be set in order to use the paddles properly. Because there are four paddles and two controllers ports, and a myriad of input devices, paddles are assigned independently of joysticks. Every time a game is cold reset, paddles are re-assigned. The core will assign paddles in order, when a port has paddles enabled. The various devices are recognised under these conditions:
Please note that some games do not use paddle 1A for their input, some exceptions are:
To make dealing with this easier, there is an option to swap paddles A and B of either port, so that 1A will become 1B and vice versa. Additionally, if the input type is set to "auto" with 2600 games, pressing the fire button will toggle the input into Joystick mode, and pressing the paddle button will toggle the input into Paddle mode, for convenience.
Over the years several Atari joystick to USB adapters have been created for 2600 and 7800 peripherals. Some of these do not split paddle operations into two distinct devices. For this scenario, a special option has been added in the periphal configuration section of the menu that allows multiple paddles to be on the same controller. When this mode is enabled, the first axis on a controller seen will be mapped as the first paddle, and the second axis moved will be mapped as the second. The first paddle button will be the assigned "Paddle" button, and the second paddle button will be the Fire II button. This is not a good user experience and I apologize for this, but there is nothing further that can be done on the matter without the framework properly splitting the paddles into two distinct devices. Also worth noting is both paddles MUST BE MAPPED AS AXIS AND BUTTONS ON THE MAIN MENU before they will work in the core.
Some games use the difficulty switches to control their behavior, most notably Tower Toppler, which will continue to skip levels if the switches are in the "low" position. For 2600 games it is important to refer to the game manual for switch positions as some games will not behave correctly if the switches are in the wrong position, and there is no pair of positions that is correct for all 2600 games. Tower Toppler also relies on composite blending artifacts to draw correctly, so it may be worthwhile to enable that for this game. The 7800 had issues with color consistency depending on the temperature of the system. Not all games may look ideal with the warm palette, so you may have to experiment per game to find the ideal colors.