The Museum of the Sierra Gorda is the best first stop if you want Jalpan to make sense. Housed in a historic building near the centre, it lays out the region's Indigenous past, mission period, and mountain culture in a way that gives the nearby churches more weight.
It is not a large museum, but it is useful. Visit before the mission churches if you can, especially if the Sierra Gorda is more than a quick detour on your route through Queretaro.