When Viola disguised herself as Cesario, she did that with a particular purpose - which was to find her brother and be close to him. She couldn't do that as a woman, which is why she decided to disguise herself as a man and start working for Duke Orsino. This creates comic situations because she is tasked by the Duke to go and woo Olivia on Orsino's behalf, however, Olivia falls in love with 'Cesario,' whereas Viola is in love with the Duke. This is both a comic situation and the main source of conflict because there is a lot of confusion about who loves whom and who should be in a relationship with whom, given that Viola is not really a man.