This quote comes from the very beginning of Chapter 14. What Jim is saying here is that he thought that it was all over for him when he was stuck on the river boat (the Walter Scott) and found the raft was gone.
When he says that it was "all up," he means that it was all over. And the "anyway it could be fixed" part means "no matter what."
So he's saying he figured that either way, he was in trouble. If he got rescued, he would be put back into slavery. If he didn't get rescued he would die -- both were bad options so it was all over for him.