Hello,
what you can do is that for each menu item you have, you let JoomSEF generate its SEF url. For static content, this will be probably based on the content title.
After the SEF URL is generated, you can edit it via JoomSEF Control Panel, View/Edit SEF URLs function (or alternatively custom). If you do that, JoomSEF will use any URL you define there. By default, when you change it, it will be saved as "custom link" (there is a checkbox for that), so it will not be deleted when you prune the auto-created links and you do not need to recreate.
Just in case you are reinstalling JoomSEF (not by auto-update but via un-and-reinstall), remember to backup your custom redirections. There is a function for that as well.
Best regards,
ARTIO Support Team