For testing purposes, I have my control PCB wired up to a set of pin headers on a scrap of protoboard. With the final joint, these pcbs need to have minimal wiring, but still be programmable. I usually use a Tag Connect for such things, but in they case I don't have space even for its small footprint, so I had to build a custom jig.
The photo above shows the completed jig. It was 3d printed so it matches the board connections perfectly, and then I used epoxied pogo pins to provide the electrical connection. All the programming pins are then attached to a standard AVR 6-pin ISP connector.
The jig design can be found here: https://cad.onshape.com/documents/3d72c1363b3b97e9fba5bf9c/w/46b2c15d39435988e5901c52/e/a0c99f7b3034ac30eab60ba3