Multi sites: how to give each site a home single entry?
It's well explained in your section settings in the CP: there is a table with the settings for each site with a hint to leave the field blank if it should be the homepage.

If you want to have a different entry as the homepage for another site create a new single section for that site.

Single Entry 1

-----------------------------------------------------
| site              | url            | template     |
-----------------------------------------------------
| english, disabled |                |              |
| german, enabled   |                | index.twig   |
-----------------------------------------------------


Single Entry 2

-----------------------------------------------------
| site              | url            | template     |
------------------------------------------------------
| english, enabled  |                | index.twig    |
| german, disabled  |                |               |
------------------------------------------------------


That way users won't be able to edit the homepage entry from other sites.
Another approach would be to limit the site permissions for your editors so they'll only be able to edit the elements which are connected to their site.