Your question is not completely clear as you have not specified what the group operation is.
However from looking at your question, I think that your group $G$ is the group of units modulo 16. This is sometimes denoted as $ \mathbb{Z}_{16}^{*}$. The binary operation is multiplication mod 16.
Now assuming this is the group you mean, I will now work through your question.
The group generated by $\langle 3 \rangle $ does indeed consist of $\{1,3,9,11\}$. As your group $G$ is abelian, you know that the subgroup $\langle 3 \rangle $ is normal, and so the quotient is well defined.
You have then correctly found the two cosets of $\langle 3 \rangle$ in $G$ (or put another way, the two elements of the quotient group).
In your question you refer to these as two groups, but this is incorrect, these are two elements of a (quotient) group. Alternatively you might refer to them as cosets (of $\langle 3 \rangle$ in $G$ ). Notice that in general a coset of $G$ is not a subgroup of $G$, for instance ${5,7,13,15}$ does not contain the identity element.
Now I think what your question boils down to is what representatives can you pick. Well you can pick anything that is in the coset as a representative, although sometimes there is a natural choice.
Notice $\{1,3,9,11\}=1 \cdot \langle 3 \rangle = 3 \cdot \langle 3 \rangle = 9 \cdot \langle 3 \rangle = 11 \cdot \langle 3 \rangle $ .
So here you could pick as your representative any of $1$ , $3$, $9$ or $11$.
And $\{5, 7, 13, 15\}= 5 \cdot \langle 3 \rangle = 7 \cdot \langle 3 \rangle = 13 \cdot \langle 3 \rangle = 15 \cdot \langle 3 \rangle $ . Here you could pick as your representative any of $5$ , $7$ ,$13$ , $15$.
Sometimes a more natural choice will become apparent, for instance if you have a coset containing even numbers and another containing odd numbers, perhaps $0$ and $1$ would be a natural choice, however you could of course choose something else!
I hope this helps and that I have correctly understood what you are asking.
For some further reading on this please see the following:
A very similar example
Is a coset a subgroup?
Canonical coset representatives