Everything will be okay.
It seems that Mercurial is smart enough to ignore subdirectories which already have repositories in them. Here's a conversation with it:
$ mkdir outer
$ mkdir outer/inner
$ mkdir outer/sub
$ echo red >outer/red.txt
$ echo blue >outer/inner/blue.txt
$ echo green >outer/sub/green.txt
$ cd outer/inner/
$ hg init
$ hg add
adding blue.txt
$ hg commit -m "create inner"
$ cd ..
$ hg init
$ hg add
adding red.txt
adding sub/green.txt
$ hg commit -m "create outer"
$ hg status
A red.txt
A sub/green.txt
$ hg commit -m "create outer"
As you can see, when i add to the outer repository, it ignores the inner directory.
If you wanted to be extra sure, you could add the inner directory to your .hgignore
.