Disclaimer: I spend very little time configuring emacs these days, as it's working well for me, and there are others around who are much better at emacs than I am. There are likely better ways to do everything than I have, but I shared what works for me.
I've got the `(add-to-list 'load-path "~/.emacs.d/lisp/")` pretty early in the file. You can put the `(require `ido) (setq ido-enable-flex-matching t) (setq ido-everywhere t) (ido-mode 1)` where you like. Basically, you just need the lines in your .emacs file - if you add the reference prior to creating the directory and populating it, you'll get an error, but nothing will break. Add the directory and do a `M-x eval-buffer` and it'll pick it up without restarting emacs. Or just restart emacs. Hope this helps. Someone will tell you a better way.