For magit, I like having it display full screen (deleting other windows), and then on quitting restore to the windows/splits I had before:

     (setq magit-display-buffer-function 'magit-display-buffer-fullframe-status-topleft-v1)
     (setq magit-bury-buffer-function 'magit-restore-window-configuration)

For more general display-buffer tweaks, OP has a whole article on it https://www.masteringemacs.org/article/demystifying-emacs-wi... (though for display-buffer I just stick to the defaults myself, never tried CIDER)

There is definitely a system to it. Something like "split at the longest side of the current window" or so. I have developed a feeling for where my magit buffer will show up. 95% of the time I am right and my eyeballs already move where it will appear. Anyway, if you want to get rid of some window/undo a split: C-x 0.

Add something like this?

    (add-to-list 'display-buffer-alist
          '("\\*Magit*\\*"
            (display-buffer-reuse-window display-buffer-in-direction
            (direction . bottom)
            (window . root)
            (inhibit-same-window . t)))*

This thread is on the "Mastering Emacs" book and from its author, on the topic of mastering Emacs window managements you can read this:

https://www.masteringemacs.org/article/demystifying-emacs-wi...

To be honest I've never played with this part of Emacs. The way I use it I'm fine with the default. But if not it's possible to take control of Emacs internal windows management.

I have my Emacs setup to never split anything and just use the whole frame (window). That also goes for things like helm. Instead of splitting I prefer to open multiple frames and let my window manager, manage them. This really improved my workflow.

How do I go about doing this ?

Seems potentially workable. Youd just jump back to the last buffer a lot of time, but that's quick and intuitivr.

(setq display-buffer-base-action '(display-buffer-same-window))

thank you ! I'll see how it goes. Hope it won't be too wonky.

Ex: In Magit when committing it now first shows a "changes" buffer that you have to kill and then you can get to the buffer where you write the commit message. Not a biggie but prolly breaks the original UI design

Same here, but I let most things replace the current buffer. Magit always fills the frame though.