。
She asked where the house was.
Literal
She [topic-は] that house [subject-が] exists place [object-を] asked.
その家のある場所 is a tidy little relative-clause structure: ある ('to exist') modifies 場所 ('place'), giving 'the place [that] [the house] exists'. The が inside the relative clause marks 家 as the subject of ある, which is conventional inside Japanese relative clauses where the modified noun is the location, not the existing thing. The whole phrase becomes the object of 尋ねる. Alternatively the same idea could be phrased as ~の場所 ('the house's location') without the relative clause; the ある version is slightly more deliberate and sounds polished.