Stories of miracles should be understood literally as historical accounts of what happened.
When a miracle is needed, Hashem directly intervenes in nature, momentarily violating or suspending the laws of nature.
The Snake in the Garden of Eden – R. Saadia Gaon gives an extensive explanation of how Hashem took a regular snake, and miraculously changed it's nature to be humanoid, with human intelligence, understanding of morality, and the ability to speak.
Stories of Angels – According to this approach, there is nothing wrong with physical manifestation of angels. However, due to other hermeneutical considerations, certain stories may be explained in ways that avoid such physical manifestation.
4 The Plagues in Egypt – Malbim explicitly states that the plagues were supernatural, and that various details in the story prevent one from understanding the plagues to have been caused by a natural chain of cause and effect.
Divine Providence – Ramban has an extremely expansive understanding of divine intervention, viewing everything that happens in the world as caused by divine providence.
Purpose of Miracles – Ramban differentiates between two classes of miracles. The large and famous miracles, such as the exodus from Egypt, are intended as proofs of Hashem's existence, that He created the world, and His continuous providence. Meanwhile, the hidden miracles, such as rain, sickness, childbirth, and even peace or war, are intended as reward and punishment.
Mutable Nature – Ramban views miracles as proof that nature is not unchanging, and therefore that the belief in the eternity of the world is false.
What is Natural? Ramban understands all of nature to be directly caused by Hashem, and therefore he classes even mundane events such as birth, rain, or war as miraculous.
All miracles were preordained during creation, and the laws of nature contain specific exceptions for each and every miracle.
The Snake in the Garden of Eden – The Mishna in Avot does not mention the snake as one of the miracles preprogrammed during twilight of the sixth day of creation.
5 However, the Rambam views this list as non-exclusive, stating that all other miracles were preprogrammed during other parts of the process of creation.
The Plagues in Egypt – Among the artifacts created on the twilight of the sixth day was Moshe's staff, which would imply that the plagues (and all the other miracles caused by Moshe's staff) were all prepared during creation.
Splitting of Yam Suf – Bereshit Rabbah states that the splitting of Yam Suf was prearranged on the second day of creation. Rambam expands this predetermination to also include the various splittings of the Jordan.
Manna and Quail – The manna is mentioned in the list in Mishna in Avot. The quail, however, are not mentioned, presumably because the quail were viewed as a natural phenomenon augmented or directed by Hashem, and not supernatural themselves.
Bilam's Donkey – Bilam's donkey's ability to speak is one of the cases of preprogrammed miracles mentioned in the Mishna in Avot.
Stopping of the Sun at Givon – Bereshit Rabbah lists the sun and moon stopping for Yehoshua among the miracles commanded during creation.
Mutable Nature – According to Rambam, nature is immutable, and therefore all miracles must have been set in nature from the day of creation.