I found a way to do this using Drush and Localization Update.
Install Localization Update
Configure a local path for po-files (admin/config/regional/language/update)
Configure automatic updates from remote servers or just local sources
Now you can put your own po-files in a local path (for example sites/all/translations). If you have translations for your own module then you name it according to this naming convention:
modulename-version.language.po
So a Swedish po-file for 'my_module', version 7.x-1.1 would be named:
my_module-7.x-1.1.sv.po
Now you have everything setup and you can start updating your sites translation with Drush:
drush l10n-update-refresh // Looks for new po-files
drush l10n-update // Updates translations