I'm confused on which way to solder the tube board to the main board. It says solder side, is this for the pins, or the socket. Or do I align the square traces on each board?
The "Solder side" label on the daughter board refers to the tube socket. The header pins that connect the daughter board to the main board are actually soldered on the other side of the daughter board. On the main board, the header pins are soldered on the component side. Yes, square holes connect to square holes. The build doc has pictures from several angles: https://www.madbeanpedals.com/projects/_folders/Tube/pdf/Archibald.pdf