Brecht uses these poems/songs throughout the play to foreshadow events, as well as drive home the themes he wishes to present. One of those themes is the reality of the horrors of war. This particular poem is directed at the captains of the brigades. It asks several questions, all connecting to the idea of what war is really like. Note the details here:

With crawling lice and looted cattle,
With lumbering guns and straggling kit -
How can you flog them into battle
Unless you get them boots that fit?

This is meant to be ironic. While at first glance it seems to be praising Mother Courage for her smart business sense during wartime, it is actually pointing out the futility of it for the soldiers. What do new boots matter to men covered in lice, struggling to carry heavy weapons, as they're whipped into battle? The answer is they don't.

The repeated refrain highlights the cyclical nature of war and peace, the never-ending waste that war produces.

The new years come. The watchmen shout.
The thaw sets in. The dead remain.
Wherever life has not died out
It staggers to its feet again.

So the soldiers that die are replaced, and the war continues ever onward. Nothing any individual does will affect this process, and those fighting the battles become faceless and nameless over time. And Mother Courage appears throughout it all, seeing a constant need for her goods. Brecht acknowledges her role, noting that her products make war just a little less hellish.