References (internal or external) are part of the sentence, set parentheses like you would do with other interjections:
"…which you can find in Eq. (1)"
vs.
*"…Which you can find in (Eq. 1)",
but:
*"In Einstein's equation for special relativity Eq. (1)…"
vs.
"In Einstein's equation for special relativity (Eq. 1)…"