Here's the outline of a proof that there exists a countable set of quadratics that partitions all the integers. There are a couple of small holes, but I think the idea should work.
The core idea is to build such a partition sequentially, adding a new quadratic $f_{n}(x)=a_nx^2+b_n$ while making sure that there's no possible way it can share any elements of its range with previous quadratics.
Specifically, start with $a_1=3, b_1=1$ and the quadratic $f_1(x)=3x^2+1$; then the range of $f_1$ is $S_1=\{1, 13, 28, \ldots\}$ and its complement is $C_1=\{2, 3, 4, 5, \ldots\}$.
Now, at each step $n$ we'll choose $b_n$ to be the smallest value of $C_{n-1}$; note that this ensures by induction that the smallest member of $C_n$ is $\gt n$ and thus that every number will fall into some $S_i$.
To make sure that we don't intersect any of our already-existing quadratics, we have to make sure that we never have $a_nx^2+b_n=a_iy^2+b_i$ for any $i\lt n$ and any integers $x,y$. But this is the same as the equation $a_nx^2=(b_i-b_n)+a_iy^2$. Note that this implies that $a_nx^2\equiv (b_i-b_n)\pmod {a_i}$. But now, if $\gcd(a_n, a_i)=1$ (and we can ensure this; in fact, we can ensure that $a_n$ is prime for all $n$) then this is the same as $x^2\equiv a_n^{-1}(b_i-b_n)\pmod{a_i}$; in other words, $a_n^{-1}(b_i-b_n)$ is a quadratic residue. But there are quadratic non-residues modulo every prime — so if we choose $a_n$ such that $a_n^{-1}(b_i-b_n)$ is a quadratic non-residue mod $a_i$, then we can be assured that the quadratics $a_nx^2+b_n$ and $a_ix^2+b_i$ will never cover the same integer. (This is where the hole is: we may have $b_n\equiv b_i\pmod {a_i}$, so that $(b_i-b_n)\equiv 0$ and there's no way of multiplying to get a quadratic non-residue. But I think a slightly smarter selection of the $a_i$ should be able to cover this gap.)
Now, this only defines $a_n$ (strictly speaking, $a_n^{-1}$) modulo $a_i$; but by the Chinese Remainder theorem (along with the fact that we've chosen all $a_i$ to be prime), we can choose $a_n$ to satisfy the congruences modulo all $a_i$ for $i\lt n$ simultaneously — and by Dirichlet's theorem on primes in arithmetic progressions, we can choose $a_n$ to not just satisfy the congruences but also to be prime itself. This lets us continue to the next $n$ in our iteration, and (in the limit) to cover all the natural numbers disjointly.