Yes, I pour the used back into the new and periodically toss the whole batch. If I've done a particularly long processing session (film or prints) where I've likely exhausted the fixer that I've taken out, though, I don't pour it back into the stock bottle.

If you do two-bath fixing for prints, you could have one for batch A that gets tossed when it is exhausted and promote batch B to A and start a new B, so that would be three bottles going at once.

I don't use the same batch for both film and prints, to avoid print staining from things that come out in the film fixer like antihalation dyes or pyro stain.