Install WordPress in domain.com and make it mimic the main site
Then create the following subsites:
domain.com/subdirectory1 will be recreated as subdirectoryA and so on.
Once you've finished, rename subdirectory1 to subdirectory1.old, and go in to Network Admin -> Sites and Edit subdirectoryA
Change the 'Path' to subdirectory1, check the box to change home and site URL, and click update.
Then run a search/replace on your database: Look for domain.com/subdirectoryA and replace with domain.com/subdirectory1
1) Keep the temporary subdirectory names the same length as the real ones. If you're using domain.com/jobs, then make the site on WP be domain.com/job1 - The length needs to match to make this easiest.
2) Make sure to check that box to change home and site URL. Very important :)
3) When you do that search and replace, looking for the domain as domain.com/subdirectoryA ensures that you wont' have false positives.
4) A nice cold drink after a hard day work is nice.