Yeah, submodules are probably what you want. Another option would be to have your working copy in a subdirectory and then point symlinks from you home directory to the files of interest.
If I understand what you're doing, you can handle it all in one repository, using separate branches for each machine, and a branch containing your common home directory config files.
Initialize the repo and commit the common files to it, perhaps renaming the MASTER branch as Common. Then create a separate branch from there for each machine that you work with, and commit machine-specific files into that branch. Any time that you change your common files, merge the common branch into each of the machine branches and push to your other machines (write a script for that if there are many).
Then on each machine, checkout that machine's branch, which will also include the common config files.
RichiH wrote a tool called vcsh which a tool to manage dotfiles using git's fake bare repos to put more than one working directory into $HOME. Nothing to do with csh AFAIK.
However, if you did have multiple directories, an alternative to git-submodules (which are a pain in the best of circumstances and this example usage is not the best of circumstances) is gitslave which leaves the slave repos checked out on the tip of a branch at all times and doesn't required the three step process to make a change in the subsidiary repo (checkout onto the correct branch, make & commit the change, then go into the superproject and commit the new submodule commit).
So the options for git come first, then the command, then the git command's options. You could easily enough alias a git command like:
#!/bin/sh
alias gitone='git --git-dir=.gitone'
alias gittwo='git --git-dir=.gittwo'
So you can commit to one or the other with a bit less typing, like gitone commit -m "blah".
What appears to get trickier is ignores. Since .gitignore normally sits in the project root, you'd need to find a way to switch this as well without switching the entire root. Or, you could use .git/info/exclude, but all the ignores you perform then won't be committed or pushed - which could screw up other users. Others using either repo might push a .gitignore, which may cause conflicts. It's not clear to me the best way to resolve these issues.
If you prefer GUI tools like TortoiseGit you'd also have some challenges. You could write a small script that renames .gitone or .gittwo to .git temporarily so these tools' assumptions are met.
For the files on the main repositories you would need to symlink each one of them, also adding them to repository .gitignore to avoid noise, unless you want to it.
Disclaimer: This is not advertising. I'm the developer of the provided library.
I've created a git extension to handle cases where you want to mix multiple repositories into one folder. The advantage of the lib is, to keep track of the repositories and file conflicts. you can find it on github. There are also 2 example repositories to try it out.
Yes, it is possible to have two git repositories in one directory.
I'm assuming that one remote repository is in GitHub and the other in GitLab. I'm also using two different SSH keys to connect to these remote repositories.
You can have both remote repositories in one of GitHub / GitLab (and use a single SSH key) - not much would change.
Pre-requisites:
Public SSH keys (id_ecdsa.pub / id_rsa.pub / id_ed25519.pub , etc.) are present in your GitHub and GitLab profiles
Private SSH keys (id_ecdsa / id_rsa / id_ed25519 , etc.) are added and persisted in your OS's keychain
SSH config file has keys specified for GitHub and GitLab: