In attempting to understand the poem, it's necessary to know what Herbert means by "mortification." Essentially, he's referring to the conscious suppression of our bodily desires and appetites. We must turn away from them, thinks Herbert, and reflect instead upon our inevitable deaths.

Throughout our lives we pass through a series of stages—infancy, adolescence, adulthood, and old age. If we reflect for a moment we will see that each stage points in some way towards our deaths. Symbols are crucial here; they foreshadow death in quite unexpected ways. So for example, when babies are born, they're wrapped in swaddling clothes. For Herbert, this is reminiscent of the winding-sheets used to wrap dead bodies before they are buried.

When we move on to our young adult years, the last thing we want to think about is dying. As well as being morbid, it's all just so far away. Yet even in our carefree youth, there are hints of what is to come in the dim and distant future. The music made by happy, pleasure-seeking youths foreshadows the grim tolling of the bell that will one day accompany our funerals:

When youth is frank and free, And calls for musick, while his veins do swell, All day exchanging mirth and breath In companie ; That musick summons to the knell, Which shall befriend him at the houre of death.

Once we reach adulthood, we are primarily concerned with settling down, getting a job, maybe even getting married. But as we busy ourselves in the details of everyday life, reminders of our ultimate end are ever-present. The world which we build for ourselves—the world of home, hearth and family—seems quite cosy on the face of it. But in actual fact, it points towards the peace and enclosed security of a casket six-feet-under.

Then, finally, we enter into our twilight years. Old age, of its very nature, involves physical, and often mental, degeneration. In relation to the former, seniors with mobility issues need to be carried around in a chair. For Herbert, this foreshadows—yes, you've guessed it—our imminent demise. Being carried around in a chair is eerily redolent of a bier—a frame on which a coffin is placed—being carried to the grave by pallbearers.

One of the key characteristics of metaphysical poetry, of which Herbert was a notable exponent, was the use of the conceit, or extended metaphor. In "Mortification," the conceit is that our whole life is like one long funeral ceremony. The very moment we're born, we start to die. And the various stages of life, which we all experience, point towards a mortality that is always there, even if we try our level best to escape from it:

Man, ere he is aware, Hath put together a somemnitie, And drest his herse, while he has breath As yet to spare.

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.