How does word order affect the meaning of a sentence
I think different word orders put emphasis on different topics. 你昨天付了钱吗 is a normal sentence so I don't think there is a particular emphasis on anything.

昨天钱你付了吗, however, put the object in front, so it's emphasizing the object and the verb rather than the subject. 

I think 昨天钱付了吗你 is the same as 昨天钱你付了吗, but using a 倒装 to, still, put an emphasis on the verb-object information.