Yeah my dotfiles, notes, and scripts are in a single repo. I think the most important thing to do is organize. I just match the system. So I put everything that a rc file in ~/ in one directory and everything in ~/.config in another. Then if you have your repo downloaded all you need is to run 2 find commands like this

  find "${DOTFILE_DIR%/}/configs/" \
        -maxdepth 1 \
        ! -name "*.md" \
        -exec bash -c 'ln -Fis "${0}" "${CONFIG_DIR%/}/${0##*/}"' {} \;

Another key component is to break out files. For example I have the directory ~/.dotfiles/rc_files/zsh. My zshrc file sources different files from that location. So I have a Linux file and OSX file there for anything that is specifically system dependent. If you want different configs on different machines you can check the hostname and use the same pattern!

Speaking of which, use functions! At first this is going to sound crazy but it's worth the effort and let's be honest, the effort is very low (though the initial rebase might not be depending on how messy you are)

  function _exists() {
      command -v "$1" &> /dev/null
  }

  alias_ls() {
    alias_lsd() {
        alias ls='lsd'
        alias la='lsd -A' # A drops . and ..
        alias ll='lsd -l' # h is automatic
    }
    alias_base_ls() {
        alias ls='ls -v --color=auto -h' # numerical sort, color, human readable
        alias la='ls -A' # ignore . and ..
        alias ll='ls -lh'
    }
    if ( _exists lsd );
    then
        alias_lsd
    else
        alias_base_ls
    fi
  }
  main() {
    alias_ls || echo -e "\033[1;31mls aliasing fucked up!\033[0m"
  }
  main

  1) debugging gets so much easier
  2) you know where everything is and what everything does. 
  3) trying new aliases, command tools, scripts, etc also becomes a lot easier. 

Since we're speaking of bash, bookmark this website: https://mywiki.wooledge.org/BashPitfalls

Fwiw, my main language is Python but for pretty much everything in the terminal I write in bash. You can often make oneliners that would traditionally be a lot of lines in Python. Not to mention it's usually faster. It's a good way to help you learn bash too! ^__^

Thanks for the detailed reply, examples, and links! Yeah, I definitely rely heavily on bash script functions, but had never thought about using git to share or sync my scripts and little programs. Thanks again, I really appreciate it!