It is clear that the speaker in this sonnet is happy to receive the flowers that her "Beloved" has worked incredibly hard to pick these flowers throughout the entire year, and has made sure that they have been installed in the room as if they had grown there:
...and it seemed as if they grew
In this close room, nor missed the sun and showers.
However, where possible confusion may lie is the way that the speaker then goes on to use the flowers she has received as a metaphor for her thoughts and desires which she, just as she has been given the flowers, "gives" to her beloved in the form of her poetry for him to look after, tend to and care for them:
...take them, as I used to do
Thy flowers, and keep them where they shall not pine.
Instruct thine eyes to keep their colours true,
And tell thy soul their roots are left in mine.
Thus, having received the flowers from her beloved which delights her, she gives back the kind of "flowers" that she can produce--her thoughts and desires expressed in her poetry, for her lover to tend to and care.