How can I configure it so that when I create and edit files in emacs the formatting looks the same in editors such as Geany or gedit,, it seems that the indentation is never preserved correctly.
This is probably related to tab ('\t', 0x9) characters. To forbid emacs from adding tab characters, customize indent-tabs-mode to nil. (C-h v indent-tabs-mode). To replace all tabs in existing files with spaces (and keep it looking as it currently does in emacs), use M-x untabify (acts on the current region).