As long as you can type code in the REPL and get it evaluated then it shouldn't matter if the window split is vertical or horizontal, that's just how emacs decided to layout its windows. If you want to have them side by side try with "Control-x 0 Control-x 3".
Just to be clear, emacs has nothing to do with Clojure, it just so happens that the Clojure community early on embraced emacs as one of its preferred editors due to its lisp support. There are other editors and IDEs that might feel more familiar to you if you don't want to learn both at the same time and support Clojure via plugins: Visual Studio Code has Calva, IntelliJ has Cursive, etc. I'm not trying to discourage you from learning emacs, it's a fantastic tool if you can invest in learning it, but it can be a daunting task to learn both emacs and Clojure at the same time.