There are normally config files for GTK at ~/.gtkrc-2.0 and ~/.config/gtk-3.0/settings.ini.

Qt themes are configured differently. For Qt5 and Qt6, set the environment variable QT_STYLE_OVERRIDE. If you still use Qt4 for anything, config is done in ~/.config/Trolltech.conf. Refer to the ArchWiki for help.

I personally prefer GUIs, though, so I'd recommend the following:

• For GTK 2 & 3: LXAppearance
• For GTK 3 & 4: Gradience
• For Qt: qt5ct, qt6ct, and/or Kvantum

I would figure out your environment variables first. It's likely based on what you're saying that your setting those variables only for interactive shell and not someplace where they are sourced by your WM or whatever is launching your WM.

Check out this section of the ArchWiki article. The rest of the article may also have some useful info.