Mortification can mean to be embarrassed, but in this poem it refers to two other meanings. One is that mortification is the suppression of the body's natural desires and appetites, a self-discipline. In Christianity, and other religions, this is a practice of self-discipline and a practice in modesty. This was called "mortifying the senses." This practice was a sacrificial exercise but also, in mortifying the senses in terms of death/mortality, it was an acknowledgment of the inevitability of death.
In this poem, Herbert presents various phases in life that contain signs which foreshadow the inevitability of death. In the first stanza, the baby is swaddled in "winding sheets" as if he is being prepared for a delivery (consignment) to death. In the second stanza, the speaker has moved to childhood. When boys sleep in their beds, it is similar to lying in a grave. Only their breath "Makes them not dead." Herbert uses the rhyme scheme (abc abc) to connect "breath" and "death" in the third and sixth lines of each stanza. This structurally establishes the ideas that there are signs of death in life and, moving to the last two lines, that there will be existence of life (afterlife) in death.
In the third stanza, our youthful years are our most energetic. The "music" could be metaphoric for the vibrancy of this phase of life. That music is connected to the last bell (knell) signaling death. As an adult, a man gets a house and this enclosure is similar to a coffin. In the next stanza, the thaw (metaphorically) drowns man's breath and, melting away the years, the biere is revealed. (A biere is pedestal upon which a coffin sits.)
Thus, man, throughout his life has created a ritual practice (a solemnity), a ritual or preparing for death.
As God teaches, these events in life foreshadow death, (death in life); the speaker supposes that this will be followed by the reverse: a life (afterlife) in death.
Yet Lord, instruct us so to die
That all these dyings may be life in death.
Each of these instances of death-signs (in life) are metaphoric. But since metaphor means to transfer the meaning from one context to another, this is particularly significant since Herbert is transferring the meaning of death (rituals, mortification) in life to death itself. And, following that, mortal life would be transferred to another context: the afterlife.