Where is the FlixBus station located and what's the best way to get there from our hotel on Rue Cler?
There are at least three Flixbus stops in Paris. When you click on one journey or another, you will see the address of the Flixbus stop or station, and you can put that into Google Maps, Apple Maps, or your preferred app to see how to get there and also how near or far that stop is from your hotel. Note that not all Flixbus stops are at stations. Some are more or less by the side of a street, like a municipal bus stop. I don't know this about Paris specifically, but I'm speaking in generalities about Flixbus in Europe.
Depending on your destination, here are the FlixBus terminals and bus stops in Paris. If your departure point is the Paris (Bercy Seine) terminal, it's a large bus station located underground.
Looking at the page linked by JoLui all of the stops listed other than Bercy are pretty far from central Paris. I would definitely make sure you book to Bercy.
If your end point for the Flix Bus is Bercy, I'd take a taxi to the Rue Cler area.