Although it's not taken literally, I find that it's used if you're going to make a submission or a presentation, etc. Naturally it means more than the orthography (literal sense). It means all the details.
This contract is very important to us, Smith. Make sure you dot all you i's and cross all your t's before you submit the plan.
Good luck with your Power Point presentation! I hope you've got all the i's dotted and the t's crossed.
Police Superintendent: We must get a conviction! I want all the i's dotted and the t's crossed before we go to court.
These days, where no one writes manually, it might be more appropriate to say "capitalize your I's and spell out your u's and r's".