Let $G$ be the nilpotent Lie group consisting of matrices $$ \begin{pmatrix} 1 & a_{12} & \cdots & a_{1,n}\\ 0 & 1 & \ddots & \vdots\\ \vdots & \ddots & \ddots & a_{n-1,n}\\ 0 & \cdots & 0 & 1 \end{pmatrix} $$ where $a_{ij}\in\mathbb R$.
I would like to find a presentation of the group $\Gamma=G\cap\mathrm{GL}_n\mathbb Z$.
The entries on the superdiagonal play a crucial role, in that the $n-1$ matrices with a single $1$ on the superdiagonal ($1$s on the diagonal and $0$s elsewhere) generate all of $\Gamma$.
Trying to write down a presentation, I would start by choosing $n-1$ generators, $a_{12},\dotsc,a_{n-1,n}$ (named after the matrix entries). It is also clear that we need commutation relations, like $$ [\cdots[[[a_{12},a_{23}],[a_{23},a_{34}]],\ldots]\cdots]=\cdots=e. $$ (If $n=3$, this would just be $[[a_{12},a_{23}],a_{12}]=[[a_{12},a_{23}],a_{23}]=e$.) I am just not sure, though, if I explicitly need to require that, say, $$ [a_{12},a_{34}]=e, $$ which seems to be directly related to the embedding I am thinking of. I would like a presentation in which any generators can be mapped to any of the matrices with a $1$ in the $(i,i+1)$ position. Is this possible?
I assume that when you are using $a_{ij}$ to denote an element of $\Gamma$, you mean the identity matrix with an extra 1 in the $(i,j)$ position.
It is easy to write down a presentation of $\Gamma$ on the $m := n(n-1)/2$ generators $a_{ij}$ with $i<j$. Just use the $m(m-1)/2$ commutator relations $[a_{ij},a_{jk}] = a_{ik}$, and $[a_{ij},a_{kl}]=1$ when $j \ne k$, $i \le k$, and $j<l$ when $i=k$. Of course many of these relations are redundant.
To get a presentation on the generators $a_{i,i+1}$, you can then use the equations $[a_{ij},a_{jk}] = a_{ik}$ to eliminate all of the other generators. Doing that with $n=3$ gives the presentation you have written down.
Although many relations in this presentation are redundant, those like $[a_{12},a_{34}]=1$ between the commuting generators $a_{i,i+1}$ are definitely not redundant, because if you left one of those out, then you could make the group bigger by putting that commutator equal to a new central generator.