Yes, if your company has multiple Prepare organisations, you will have to download and install an upload-client for each organisation.
When the Prepare Upload-client starts and contacts the server thefirst 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.