What are the subobjects of a manifold?
Let $\mathcal{C}$ be the category of toplogical(resp. differential) manifolds. The objects of $\mathcal{C}$ are topological(resp. differential) manifolds and the morphisms of $\mathcal{C}$ are continuous(resp. smooth) maps.
Let $f\colon X \rightarrow Y$ be a morphism in $\mathcal{C}$. We claim $f$ is a monomorphism if and only if $f$ is injective.
Suppose $f$ is a monomorphism. Let $x, y$ be distinct points of $X$. Let $p$ be a $0$-dimensional object in $\mathcal{C}$. There exists the unique morphism $g\colon p \rightarrow X$ such that $g(p) = x$. Similarly there exists the unique morphism $h\colon p \rightarrow X$ such that $h(p) = y$. Since $g \neq h$, $fg \neq fh$. Hence $f(x) \neq f(y)$. Hence $f$ is an injective map.
Conversly suppose $f$ is injective. Clearly $f$ is a monomorphism.
"Are they the same as submanifolds?"
Generally no.
Counter-example:
Let $f\colon \mathbb{R} \rightarrow \mathbb{R}^2$ be the map defined by $f(x) = (x^3, 0)$. $f$ is smooth and injective, but is not an immersion($f'(0) = 0$). Hence $\mathbb{R}$ cannot be identified with a submanifold of $\mathbb{R}^2$ by $f$.
Monic morphisms are injections in concrete categories like the category of manifolds, so a subobject of a manifold $M$ is another manifold with an injection into $M$. This isn't quite the same thing as a submanifold, as usually submanifolds are required to be embedded, meaning that they inherit their topology from the larger manifold.
For an example of a manifold that is injected into a larger manifold but isn't embedded, let $M$ be a torus (considered as a quotient space of $\mathbb{R}^2$ under integer translations), and let $L$ be the real line, mapped to a line of irrational slope in $\mathbb{R}^2$ and then projected to the torus. This causes the line to "wrap around" infinitely without touching itself. This map is an injection, thus $L$ with this map is a subobject, but the image isn't a manifold, since any neighborhood of a point contains infinitely many "nearby" lines.
Edit: As pointed out below, I was erroneous when I said monic morphisms are injective in all concrete categories. It is true for manifolds, however, as proved in Makoto Kato's answer.