In "Holy Sonnet VI," as in other sonnets by Donne (see especially "Holy Sonnet X" -- "Death be not proud..."), the poet presents a life/death paradox. Donne views death as merely a temporary rest on the way to everlasting life. In "Holy Sonnet VI," this idea is seen most clearly in lines 4-8 when he writes, "My span's last inch, my minute's latest point ; / And gluttonous Death will instantly unjoint/ My body and soul, and I shall sleep a space ; /But my ever-waking part shall see that face,/Whose fear already shakes my every joint." Here, Donne speaks of finishing the race, which symbolically represents his life, and then "sleep[ing] a space," which is the temporary rest provided by death. Although his body has died, his soul, his "ever-waking part"will not perish. Paradoxically, though, the body must die in order for the soul to earn its eternal life.
This theme is continued in the next several lines, as well, when Donne writes, "Then, as my soul to heaven her first seat takes flight, / And earth-born body in the earth shall dwell, / So fall my sins, that all may have their right, / To where they're bred and would press me to hell" (9-12). Again, Donne emphasizes the separation of the body and soul and the necessity of bodily death to achieve eternal life of the soul. His body remains "in the earth" (in the grave), while his soul flies "to heaven," leaving the sins of mortal life behind forever. For Donne, this is a joyous occasion. While on earth, sin threatens to damn him, so sloughing off that sin as his soul ascends makes Donne feel free. It may be natural to fear death, but Donne's religious beliefs instead cause him to embrace death, as it is necessary in order for his soul to dwell in eternal peace.
The paradox of the poem -- the idea that the body must endure death in order for the soul to celebrate eternal life -- effectively solidifies Donne's theme. This paradox is developed over the course of the sonnet but is succinct enough to work within the strict confines of the sonnet form.