This is likely an unsolved problem; I will provide some keywords and related references. Such a set is sometimes known as an additive basis of order 2. Related questions on mathSE are 1, 2, 3 (unanswered), and 4 (unanswered).
There are some elementary properties you can give about additive bases; for example, for such a set $S$, it must contain at least $n$ of the first $n + \binom{n}{2} = \binom{n+1}{2}$ nonnegative integers, or else there wouldn't be enough pairs to cover all $0, 1, \ldots, \binom{n+1}{2} - 1$. But an exact characterization appears to be much harder -- there are many open conjectures.
For starters, finding an exact characterization would have implications for the strong Goldbach conjecture. To see this, consider the set $S$ of numbers of the form $p - 3$ or $p - 2$ where $p$ is an odd prime. If the strong Goldbach conjecture is true, then for any $n$ either $n + 5$ or $n + 6$ is an even number greater than or equal to $6$, and thus equal to the sum of two odd primes, so $S + S = \mathbb{N}$. On the other hand, if the strong Goldbach conjecture is false, then there is some even number $n > 6$ that can't be written as the sum of two primes, and it follows that the odd number $n + 5$ can't be written as a sum of two elements of $S$. In particular, since $n + 5$ is odd, it would have to be written as an odd number plus an even number, so it would equal $(p_1 - 2) + (p_2 - 3)$ for some odd primes $p_1, p_2$.
This means that a sufficiently "simple" exact characterization would lead to a simple solution to the strong Goldbach conjecture, and such a simple characterization is thought to be very difficult to obtain.
There are other relevant open problems. For example, the Erdős–Turán conjecture concerns the number of ways $f(n)$ to write $n$ as the sum of two elements of $S$, for sufficiently large $n$. It conjectures that for any set $S$ where $S + S = \mathbb{N}$, there is no upper bound on $f(n)$ (so $f(n)$ has arbitrarily large values).
I initially found these references by writing down the number of possibilities in such a set $S$ for the elements $0, 1, 2, \ldots n$. That is, defining the notation $[n] := \{0, 1, \ldots, n\}$, we can ask, what is the number of subsets $S \subseteq [n]$ such that $S + S$ covers $[n]$? We get the sequence $1, 1, 2, 3, 6, 10, 20, 37, 73, 139, 275, \ldots$, which turns up the following result in OEIS:
- A066062: Number of distinct subsets S of T={0,1,2,...,n} such that each element of T is the sum of two elements of S.
There appear to be two other sequences in OEIS that are also equivalent (though the equivalence is not immediately obvious):
Each of these contains some additional references on this problem and related problems.