It may not cool the transmission as well, but I don't think it did any damage. I would definately get them put back where they should go though.
Did you change all of the lines? The hoses are different length and can only go where they are long enough to go to. Have you checked the How-To Docs to see the different diagrams. One of those should show where they go. If they don't, post again. I am going to change my oil in a few minutes and I will try to get some pictures of it for you. Try my locker under filter and look at those. I think there are some pictures of the lines there. The line that hooks up to the filter comes from the tranny.