The answer to your second question is the easier one, because it is purely about the structure of the Lie algebra $\mathfrak{u}(N)$:
The group $\mathrm{U}(N)$ has dimension $N^2$ and its maximal torus is a subgroup $\mathrm{U}(1)^N$. If you split the algebra accordingly as $\mathfrak{u}(N) = \mathfrak{u}(1)^N \oplus \mathfrak{h}$, and write the generators of $\mathfrak{u}(1)^N$ as $T^{ii}, i\in\{1,\dots, N\}$, then $\mathfrak{h}$ consists of $N^2 - N$ generators $T^{ij}, i\neq j$ with $[T^{ii}, T^{jk}] = \delta^{ij}T^{jk} - \delta^{ik}T^{jk}$. The physicist says that $T^{jk}$ has "charge +1" under $T^{jj}$ and "charge -1" under $T^{kk}$.
So what needs to be established is that the massless states corresponding to the strings stretching from the first to the second D-brane really transform like that under the infinitesimal transformation generated by the $\mathrm{U}(1)$-symmetries associated with the respective brane. In the end, it will turn out that we really need to put it in by hand in some sense, but maybe it's at least an interesting history lesson:
You can't really see this if you take "$N$ coincident branes" as your starting point because "$N$ coincident branes" doesn't actually mean anything! What does it mean for branes to be coincident? A D-brane was originally just the surface to which Dirichlet boundary conditions confine the endpoint of an open string - there is no mathematical content to saying there is "more than one" such surface at the same point.
So why do physicists talk about these coincident branes? It's because of $T$-duality applied to an (ancient, in string theory terms) idea:
Originally, physicists simply associated the Chan-Paton factors of a $\mathrm{U}(N)$ gauge theory to the ends of strings ad hoc - Chan and Paton were "old" string theorists for whom the string was the flux tube between a quark and an antiquark, and they simply needed to put $\mathrm{U}(N)$ groups in there because they knew or at least suspected that quarks were charged under some $\mathrm{U}(N)$ groups.
Now, we come to Polchinski et al.'s "Notes on D-branes":
During the 90s, people started to think of D-branes as dynamical objects in their own right, and realized that the Dirichlet boundary conditions could be obtained by T-duality (one dimension of spacetime is compactified as a circle of radius $R$ and we send $R\to \alpha/R$) from Neumann boundary conditions - you get a D-brane sitting at one point in the compactified dimension. So a natural question is what happens to a string with ad hoc Chan-Paton factors when you dualize it into a string with Dirichlet conditions.
If you don't do anything special, nothing. There's nothing there hinting at some stack of branes. But if you break the symmetry as $\mathrm{U}(N)\to \mathrm{U}(1)^N$ prior to applying the duality, then suddenly you get not one $D$-brane, but $N$ $D$-branes, sitting around the circle at angles corresponding to the non-vanishing angle $\theta_i$ in the order parameter (value of a Wilson line) $\mathrm{diag}(\theta_1,\dots,\theta_N)$ of the spontaneous breaking of the Chan-Paton theory. The (massive) vector states associated with strings between two different branes are charged in the $(-1,1)$ fashion under the $\mathrm{U}(1)$ on these branes because we got them by dualizing a broken $\mathrm{U}(N)$ theory.
And now, if you take the limits $\theta_i\to 0$, then you see the D-branes in the dual theory rushing towards each other, until at $\theta_i = 0$, i.e. restored $\mathrm{U}(N)$ symmetry, there's only a single position left and they "all sit on top of each other". This is the origin of "coincident branes", and so by "$N$ coincident $D$-branes", we really mean "the theory T-dual to the theory of a string with Neumann boundary conditions with ad hoc $\mathrm{U}(N)$ Chan-Paton factors.