the passage you have quoted referred to the visiting between the two Uppercross families --the elder Musgrove family at the Great House and Mary and Charles at the Cottage. They are in a comfortable walking distance from each other which would make frequent visits convenient. That is why the passage states that Anne was surprised to find Mary alone.

This is awkwardly worded ...".knew the ways of Uppercross as well as those of Kelllynch." I believe here she mentions Kellynch merely to illustrate that she is as familiar with the habits of the two Uppercross families as well as she is with the habits of her own home. It is three miles between Kellnych and Uppercross, a distance that would preclude anyone "running in and out of each other's house at all hours."