I think you use 'let' as in
Let $x$ be s.t. $P(x)$
When you know for sure that this is possible. On the other hand you use
Suppose $x$ is s.t. $P(x)$
is used when you're not yet sure/are going to derive a contradiction from here.
For example, when you want to proof that
$x$ is limit point of $A\subset \mathbb{R}$ iff $\exists\{x_n\}\subset A-\{x\}$ with $x_n\to x$
Then for the $\Leftarrow$ direction I might start by saying something like
Suppose $x$ is s.t. there is a sequence $\{x_n\}\subset A-\{x\}$ with $x_n\to x$ but $x$ is not a limit point of $A$
And derive a contradiction. I might also start by saying
Let $x$ be s.t. there is a sequence $\{x_n\}\subset A-\{x\}$ with $x_n\to x$
And then just prove $x$ is a limit point directly.
Again, I'm not sure this is the way everyone thinks about it, but to me it makes the most sense. It also makes it clear to the reader what direction the proof is going in.