A quick question for writers

I mentioned earlier that I have been using the equivalent of MS Word's wordcount while writing, and that this has not perhaps been very smart. I know that we're all looking at the lengths of our various books, and I was wondering: How do you keep track of wordcount while writing? Because I had an extra 45K words and an extra 25K words when looking at the page runoffs on the two books I did write in Scrivener, and this was ... unfortunate. And I would like not to repeat it if I can*.

If you need to turn in a 100k manuscript--or a manuscript of a specific maximum length--do you check the runoff count as part of your daily writing, do you format it in manuscript format so you write -to- a runoff count?

ETA: * I am aware that there might be a bit of gentle mockery at this point