Ok, so there were, I think, two separate issues.
One, to fix the default, no-init-script background color I removed the following lines from my Xresources file:
To fix the color issues in helm, I downloaded the doom themes. Using a doom theme ...
Something like this in your ~/.emacs will leave the terminal foreground and background untouched, i. e. emacs will use your terminal colors:
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such ...
You can also use custom-set-faces to just NOT set properties when using a tty, and then have other defaults for other types.
With the following, the default face gets foreground and background set unless the display type is tty, as it is when you run emacs -nw.
For some other things, I generally like the defaults, especially when using X11. I override a ...