Aligning different boards that connect via pogo pins

I’m designing a small mobile device which needs a separate companion device for charging, programming, and data collection. Because the mobile device needs to be pretty small, I’m planning to use pogo pins to connect the two. But as they are (currently) spaced sort of ad-hoc where there’s space, I don’t have a great way to layout the pins on the charging device so they line up correctly. What’s the standard way people develop this type of design? Duplicate the project and remove everything except the pins? One thought I had was to instead create a footprint with the number of pads I need as a dedicated connection point, which would be easy to align, but that ends up taking up a bit more space than I would like compared with inserting the pads where they fit between components.

I’m just now starting work on the charger side, so before I start that project I figured I should probe the community to see how other people would approach this.

you may find some tips here:

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You could use registration holes.

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