Is it (AとB)のC, Aと(BのC), or (AのC)と(BのC) ...?
It depends on the context.
For example, in the case of 彼と私の娘は、昨年同じ小学校に入学した. When he is a child, it means Aと(BのC). When he is an adult, it means (AのC)と(BのC). When he is the daughter's father and the sentence is 彼と私の娘は、昨年小学校に入学した, it means (AとB)のC.
In the case of 彼と私の娘は、頭が良い, it also could mean the three patterns. If you clearly want to mean (AのC)と(BのC), you should say 彼の娘と私の娘は、頭が良い.
This would probably depend on context, as in English.
For instance, I think the following sentence would be ambiguous in both English and Japanese:
I found out all kinds of things thanks to Tanaka and Shimada's notebook.
It could mean that the speaker spoke to Tanaka and read Shimada's notebook, or it could mean that the speaker read a notebook belonging to both Tanaka and Shimada.
Of course, in the vast majority of sentences, semantics would be enough to clear up any such ambiguities. Failing that, it's often possible to disambiguate using intonation (in speech) or punctuation (in written text). For instance:
A pause or comma after the first name would help to indicate that the notebook belongs to Shimada only. Similarly, a clear lack of pause between the names in speech would indicate the opposite (I don't think there's any easy way of representing this explicitly in text, but I think a lack of comma would make it the more likely interpretation.)
EDIT: I just realised that there's actually a third possible interpretation for the sentence in Japanese, which is that the speaker read multiple notebooks, one or more of which belonged to each of Tanaka and Shimada. This particular ambiguity is of course resolved in the English sentence by the use of the singular "notebook", but there's no way of resolving it in Japanese without adding extra verbal clarification, just as the English "Tanaka and Shimada's notebooks" would be ambiguous with regard to the number of notebooks and who owned which ones.
Usually ambiguities are resolved by context, and if not, then they are declared "bad writing" (or "bad expression").
In the case at hand, AとBのC can mean all of Aと（BのC）, （AとB）のC, （AのC）と（BのC） — actually just like "A and B's C" in English:
A and B's parents also come
A comes and B's parents come
(A and B)'s parents come
(A and B)'s parents come
If you are mathematically inclined, you could think of と corresponding to + and の to ×.
In mathematics, the ambiguity of A+B×C is resolved by declaring A+B×C = A+(B×C) ("order of operations"). In natural languages, there are no order of operations, so AとBのC is still ambiguous.
However, I think we usually have (2) = (3) corresponding to (A+B)×C = (A×C)+(B×C) ("distributive law").
Ambiguous contexts aside, context often gives the natural interpretation:
(A and B)'s shoes got wet. more likely interpretation
A got wet and B's shoes got wet. less likely interpretation