This is a kind of Auslander–Reiten theory; for each indecomposable summand $M_i$ of $M$, you want to find a right-almost split morphism
$\varphi\colon\widehat{M}_i\to M_i$
in $\operatorname{add}{M}$. In other words, this should not be a split epimorphism, but any non-isomorphism $M_j\to M_i$ for any indecomposable summand $M_j$ of $M$ should factor through it.
Then $F\varphi$ is a projective presentation of $S_i$ (the simple top of the projective $FM_i$), and so setting $N_i=\operatorname{ker}(\varphi)$ and using left-exactness of $F$ shows that $FN_i=\Omega^2(S_i)$.
This is typically the approach used to show the equivalence of finite global dimension of $B$ and finite $\operatorname{add}(M)$-resolution dimension in $\operatorname{mod}(A)$ (and to explicitly bound $\operatorname{gldim}(B)$ by $2$ more than this resolution dimension), and it is also used by Iyama to bound the global dimension of endomorphism algebras of cluster-tilting objects in certain cases. Unfortunately, I don't know a situation where one can bound the $\operatorname{add}(M)$-resolution dimension just of the $N_i$s without just bounding it for all $A$-modules, as in these examples, since the construction doesn't make it very easy to understand these modules.
I should add that this is just a variant on the general argument that shows any finite-dimensional $B$-module (the crucial property being that it is finitely-presented) $X$ has $\Omega^2(X)=FN$ for some $N$; under Yoneda, a projective presentation of $X$ is of the form
$$FM_1\xrightarrow{F\varphi}FM_0\to X\to 0$$
for some $\varphi$, and $N=\operatorname{ker}(\varphi)$ has $FN=\Omega^2(X)$. On the other hand, in the case that $X$ is simple, it is possible to be a little bit more concrete about the properties of $\varphi$, which might be exploitable.