A nice book that goes into these kinds of things is Goldrei's Classic Set Theory.
In regards to the specific issue you're having, a detour into the history of set theory will be instructive.
For a long time, humanity toyed with one number system, namely $\mathbb{N} \setminus \{0\}$. Then we discovered $0,$ which allowed us to discover $\mathbb{Z}.$ Then more number systems started coming along; indeed, the process eventually went into overdrive. By the beginning of the 1900's, mathematicians were looking into all sorts of crazy algebraic and relational structures. Now, they knew some ideas for mathematical structures simply didn't make sense (think: a number system where $0 \neq 1$ and $0 = 1$ both hold). So, they became concerned with the existence of structures. The idea is this: if make use of a structure $X$ to prove something about a structure $Y$, well this proof is only valid if $X$ actually exists.
The problem then becomes, how do you decide which structures are valid, and which are not? Set theory came to the rescue, because people realized that it serves as a sort of all-purpose Lego kit for building mathematical structures. (My thanks go out to Peter Smith for that wonderful turn of phrase). But the point is, once you've shown that a mathematical structure exists, the actual details of its construction cease to matter.
This has implications for the issue you are having.
Once you've shown that $\mathbb{N}$ and $\mathbb{R}$ exist, it ceases to matter whether you constructed them in such a way that $\mathbb{N} \subseteq \mathbb{R}$. The point is, there is a function $f : \mathbb{N} \subseteq \mathbb{R}$ such that $f(1_\mathbb{N} + \cdots + 1_\mathbb{N}) = f(1_\mathbb{N}) + \cdots + f(1_\mathbb{N})$, where the number of entities being summed on the left equals the number being summed on the right, and this function turns out to be the unique embedding of the natural numbers into the reals that preserves all the usual operations. We call it the 'natural embedding' (of the naturals into the reals). Whether or not $f$ is the inclusion map is entirely up to you. Indeed, you can make this choice anew, in every theorem you state and every proof you write. Just write: 'without loss of generality, assume the natural embedding $\mathbb{N} \rightarrow \mathbb{R}$ is the inclusion map.'
Thus, for example, you don't have to try to define logs of natural numbers. You do it for the reals, and whenever you need to take the log of a natural number, you make sure the reader knows that the natural embedding $\mathbb{N} \rightarrow \mathbb{R}$ is the inclusion map in this context.
Now admittedly, I do not know a formal proof that you can just simply assume, without loss of generality, that the natural embedding $\mathbb{N} \rightarrow \mathbb{R}$ is the inclusion map, or even how to formulate this concept as a theorem. But, it makes intuitive sense.
Anyway, the point is this.
You get to choose.