Do what you will means go ahead and act as you choose, said with casual acceptance or a shrug. Do what you will, I'll be here when you get back. It can also carry a resigned, dismissive tone: Do what you will, then. Don't say I didn't warn you.
The nearest confusion is do as you will, the more formal form that sounds like permission from someone in charge.
Do what you will is the everyday, casual version, said with a shrug or light resignation. The resigned reading tends to surface when the speaker has given up arguing or cannot control the outcome anyway: Do what you will, I'll be here when you get back. Someone might also use it after a debate has gone in circles, as in Fine, do what you will, just don't say I didn't warn you. In both cases the phrase signals acceptance of a choice the speaker no longer wishes to fight.
The nearby form do as you will is close in wording but sounds more formal, like permission handed down by someone in charge. If a manager says Do as you will, it can carry a tone of granted approval rather than casual acceptance.