You can't merge a repository into a branch. You can merge a branch from another repository into a branch in your local repository. Assuming that you have two repositories, foo and bar both located in your current directory:
$ ls
foo bar
Change into the foo repository:
$ cd foo
Add the bar repository as a remote branch and fetch it:
$ git remote add bar ../bar
$ git remote update
Create a new branch baz in the foo repository based on whatever your current branch is:
$ git checkout -b baz
Updated with "real-life" commands:
Start from your repo directory, make sure your working copy is clean (no files changed, added or removed).
Make a new branch:
git checkout -b <my-branch>
Add the secondary remote, then fetch it:
git remote add <repo-name> git@github.com:xxx/<repo-name>.git
git remote update
Merge one of their branches in your current branch:
git-merge <repo-name>/<their-branch>
If you don't know which <their-branch> you want, then go for master
If you are sure you want to accept all remote changes and avoid conflicts (overwrite yours) then you can specify -X theirs as option for git merge in the last step.
If you want to add it in a subdirectory then probably you should probably use git submodules
Merge branch somebranch from the bar repository into the current branch:
$ git merge bar/somebranch