おまえは おれが たおす means "It's you (, not someone else,) who I will defeat."
"I will defeat you" is おれはおまえをたおす。
は has two ways of use.
The former は is a particle that means "speaking of", the latter は is a particle attached to the subject of a sentence.
So, おまえは おれが たおす is like "Speaking of you, the person who will defeat you is me."