There are mostly quite a few differences in plot between Twelfth Night and She's The Man. The biggest difference is that Amanda Bynes's character, Viola, decides to impersonate her brother at his school while he is absent. Bynes's Viola even takes on the same name as her brother in order to carry out the impersonation. In contrast, Shakespeare's Viola, while she may have had her twin brother in mind, is only impersonating a man. She goes by the name Cesario rather than her brother's name Sebastian.
Another significant plot difference is motive behind the impersonation. Bynes's Viola wants to impersonate her brother in order to compete with the boys from her own school who forbade the girls to play soccer with them once their own program was shut down, thereby proving her soccer skills. For Bynes, Viola's motive is purely an ambitious motive. In contrast, Shakespeare's Viola has just landed in a foreign location after surviving a shipwreck and thinks she is the only survivor of her wealthy family. As a single, wealthy noble woman without any male protection, she knows she is in a dangerously vulnerable position. Hence, she decides to disguise herself in order to protect her true identity. At first she has the idea to disguise herself as a servant in the house of Olivia to protect her true identity, but when the sea captain who rescued her warns that her services would be rejected, she decides to disguise herself as a eunuch in order to work for Duke Orsino. We see Shakespeare's Viola explain her motive of self-protection in her lines:
O that I served that lady
And might not be delivered to the world,
Till I had made mine own occasion mellow,
What my estate is! (I.ii.43-46)
Another significant plot difference is that the film She's The Man does away with the madness theme and the persecution of Malvolio who is represented as a tarantula. Also Shakespeare's Viola mostly services Duke Orsino by helping him try to court Olivia. In contrast, while Bynes's Viola also tries to help Duke court Olivia, Duke does a greater service for Bynes's Viola by coaching her in soccer so that she actually has the skills she needs to be able to play with and compete against the men's teams.