As Tobias Kildetoft points out, the question does not make sense in this generality. Root systems are reasonably defined only for semisimple, or at best reductive, Lie algebras. But even a simple Lie algebra generally has tons of subalgebras which are far from being reductive. Or what would you say is "the root system of
$\mathfrak{h}:=\pmatrix{ * & \dots & * & * \\
0 & \ddots & & * \\
0 & 0 & \ddots & * \\
0 & 0 & 0 & *} \subset \mathfrak{sl}_n(k)$"?
Even if we restrict to semisimple subalgebras $\mathfrak{h} \subset \mathfrak{g}$, in general there is no reasonable map $R_\mathfrak{h} \rightarrow R_{\mathfrak g}$ between their respective root systems. For example look at the inclusion $\mathfrak{so}_5(\mathbb C) \subset \mathfrak{sl}_5(\mathbb C)$. Good luck finding a map from the root system $B_2$ to the root system $A_4$. So your statement
Nevertheless, there must be some map from the root system of the subalgebra to the root system of the original algebra because that's how embedding a subalgebra is defined.
must be based on a misunderstanding. Maybe you mean something the other way around, like "if there is an embedding of root systems $R_1 \hookrightarrow R_2$, and $\mathfrak{g}_1, \mathfrak{g}_2$ are split (say, complex) semisimple Lie algebras having the respective root systems, then there's an embedding $\mathfrak{g}_1 \hookrightarrow \mathfrak{g}_2$. (I'm not even sure if that is literally true, in any case it's non-trivial.)
But think of this: If you have an automorphism of $\mathfrak{g}$, then its fixed points form a subalgebra $\mathfrak{h}$ of $\mathfrak{g}$. In some nice examples this subalgebra is reductive or even semisimple. If the automorphism was chosen so as to stabilise a certain Cartan subalgebra, then one can get the root system of $\mathfrak{h}$ as (subsystem of) a "folding" (quotient) of the root system of $\mathfrak g$. Compare e.g. Semisimple complex Lie algebra of type $A_3$ contains a Lie subalgebra of type $B_2$ as fixed points of an automorphism., Folding and realization of type B Lie group as a subgroup of $GL_n$., Understanding $G_2$ inside Spin(7)? (EDIT: problem solved), and the comments to https://mathoverflow.net/a/244895/27465.
The main reason I bring up this class of examples is that here one does have a map between the root systems, but here it is the other way around: In the first question linked above, the inclusion $$\mathfrak{sp}_4(\mathbb C) \hookrightarrow \mathfrak{sl}_4(\mathbb C)$$
corresponds "contravariantly" to a quotient map $$A_3 \twoheadrightarrow C_2.$$
And sometimes it is even more intricate: "Folding" of $A_4$ gives the non-reduced root system $BC_2$, which has $B_2$ as a reduced subsystem. That's the connection of the root systems $B_2$ and $A_4$ that governs my above example $\mathfrak{so}_5(\mathbb C) \subset \mathfrak{sl}_5(\mathbb C)$:
$$\matrix{A_4 &\twoheadrightarrow & BC_2 \\
&& \cup \\
&& B_2}$$
You cannot express this with one map between $A_4$ and $B_2$ in either direction. So if there is any way in which one turns root systems into a category such that inclusions of semisimple Lie algebras would correspond to morphisms between root systems, these morphisms would not be maps in the standard sense: It's at least something like above, taking subsystems of quotients. (I am not even sure if that would "catch" all subalgebras. I do believe that in principle such an assignment would need to be contravariant though, i.e. to a morphism $\mathfrak{h} \rightarrow \mathfrak{g}$ would correspond a morphism $R_{\mathfrak{g}} \rightarrow R_{\mathfrak{h}}$.)
- On the positive side, one finds certain very special kinds (in particular, as you say "regular" -- a nomenclature which unfortunately is totally overused for c. 200 different things) of subalgebras by looking at (special kinds of) sub-root systems. That's the content of Borel-de Siebenthal and related theories ("Branching Rules"). You say you are interested in $E_6$, maybe this helps: https://mathoverflow.net/q/314025/27465. (On the other hand, folding gives something like a ghost of a group of type $F_4$ inside $E_6$ groups, cf. https://mathoverflow.net/q/203295/27465.)