Middle, or open C#, is one of the worst notes on any saxophone, and will take time and patience to learn how to voice. It is a bad note because it is the only note you play where no keys are being depressed ... there is very little resistance, and not much of the body tube is actively in play (for the oppoiste, think low Bb, where all the keys are closed the body is a solid tube).
Tone matching to the first overtone off of low C# is a pretty vital excercise for warming up your middle C#, as is tone matching to the notes close to it on the horn ... which includes the dreaded middle D. Ha ha! Ain't the saxophone fun!?!
Just be patient. It will take a while for everything to start to sound good ... that's normal.