Lyke as a ship that through the Ocean wyde,
By conduct of some star doth make her way,
Whenas a storme hath dimd her trusty guyde,
Out of her course doth wander far astray: (lines 1-4)
A ship traveling through a large ocean with no land in sight uses the stars to guide its way, but when stormy clouds block the star's light the ship will stray far from its course.
The "her" mentioned in this stanza is referring to the ship; in the English language most (if not all) modes of transportation are described with feminine pronouns. In this analogy, Spenser would be the ship that has gone off course, because his beloved's light is no longer shining on him. A storm is a clever way to describe an argument, because arguments can be described as being dark, angry, heated, wet (meaning crying), and other such adjectives. Astrology plays a big part in this poem and in navigation. Before the time of GPS's all you had to guide your way were compasses and the constellations. The brightest star is the North Star; however, he is not referring to that star in this poem. Instead he is referring to Ursa Major (a.k.a. Great Bear), which contains the Big Dipper.
So I whose star, that wont* with her bright ray
Me to direct, with cloudes is overcast,
Doe wander now in darknesse and dismay,
Through hidden perils round about me plast**.