Find an appropriate place on the case for the jacks. The three RCA jacks use 1/4 inch holes. The s-video jack can use a 1/2 inch hole, or use a 3/8th inch hole and enlarge it with a Dremel to fit the s-video jack. Place the RCA jacks 1.5cm apart, and place the s-video jack 2cm from the nearest RCA jack. If your modding a heavy sixer, you will need to countersink the holes for the jacks.
Find your Atari motherboard using the link above and connect the inputs on the mod board to the locations on the pictures. There are two connections that you will need to make from the main board to the output side of the mod board. One is marked VCC on the mod board, this is +5 in. Also connect one of the GND connection on the output side to the ground on the Atari. Note I used the GND connection next to the Audio Out since I shared the audio ground with composite. The picture below illustrates this on a 6 switch unit.