Yes, if your company has multiple FirstAgenda organisations, you will have to download and install an Upload-client for each organisation.
When the FirstAgenda Upload-client starts and contacts the server the first time, the Upload-client will be registered to your organisation. In this way, you can ensure that there can only be one uploader in each organisation. By using one Upload-client per organisation, you avoid data from the different organisations being mixed together.
The organisation's details are registered in the settings file.