Both are fine to use. But I use "주말 잘 보내세요" more often when I talk to friends and colleagues and "좋은 주말 보내세요" when I send a message or an email. No need to use "-에" for 주말.

Both are good, but I am personally more comfortable with the first one. 좋은 주말 sounds slightly more formal to me. In both, 주말에 is almost ungrammatical, because 보내다 (pass the time = to live / get by) is a transitive verb working on the object 주말. 주말을 is grammatically okay, but adding 을 makes them sound worse.