Transpose Clarinet in A?

So, I am playing Fidelio Overture, Op. 72 by Beethoven, and I have to transpose it. I don't really know how to transpose for sure so I have some ideas, but I really need some fast help (last rehearsal is in like an hour)... So, it is written in A for the Clarinet for some reason. They told me that the flute music which has a concert E Major. I tried transposing everything into E major, which is down a third and has two sharp notes, but a lot of notes conflict. Please help me!