You have asked a very perceptive question. Obviously, the fact that Shakespeare decided to give this play a subtitle makes us ask what relevance the subtitle has to the play at large and causes us to try to draw parallels between it and the action.
Twelfth Night was a festival in Elizabethan times that was even more important than Christmas itself. It celebrated Epiphany, the time when traditionally we believe the three kings arrived and gave their gifts to Jesus. However, in Elizabethan times it was a festival that celebrated excess and chaos. Heavy drinking, cross dressing and a topsy-turvy social order were celebrated. This was before the end of the Christmas period and the beginning of January and a new year. Traditionally we take our decorations down after Epiphany on 6th of January. So, understanding this festival more allows us to draw many parallels between the action of the play and its title. Sir Toby Belch and his cronies are celebrating to excess this festival. When he asks in Act II scene 3:
But shall we make the welkin dance indeed? Shall we rouse the night owl in a catch that will draw three souls out of one weaver? Shall we do that?
We hear the voice of a die-hard party-goer who is determined to extract the most fun and chaos out of this season. Because Twelfth Night also featured a topsy-turvy social order, we gain new understanding as to Malvolio´s hopes. Twelfth Night as a festival featured a reversal in power: servants would be waited on by their masters and there was general chaos and hilarity. This adds new emphasis to Malvolio´s hopes that he might have a chance with his mistress Olivia.
What You Will, on the other hand, represents a challenge to the audience to try and interpret or make sense of the chaotic action in the play. What message are we as an audience going to take away from the action? The title What you Will bestows the audience with the responsibility of trying to process the chaos, humour and fun they have just seen. What do we make of Malvolio? How do we interpret the way that love is seen like a disease or a sickness that we suffer from?
So, to me, both titles are important to the play as a whole, elucidating its theme and message and involving the audience in the action. Clearly both need to be analysed carefully to how they relate to the play and what Shakespeare is trying to say through this masterful comedy.