The manual update is described in this section of the documentation, step by step. Basically:
1. Uninstall the plugin via the plugin manager. (always use the plugin manager, it's the safest)
2. Download the new version
3. Install the new version
The database elements are not removed upon uninstalling the plugin, don't worry about it.
The duplicate folder issue occurs when you try to install a plugin manually 2 or more times, and wordpress does not clean up the temp folders. In that case I suggest these steps:
1. Deactivate the plugin and uninstall it via the plugin manager
2. If there are remaining duplicate folders, remove them via FTP
3. Check the plugin manager, there should be no traces left of the plugin there. If it's still on the list, then a duplicate folder is still in the plugins directory, proceeed back to step 2.
4. Now install the new version via the plugin manager
If you like my products, don't forget to rate them on codecanyon :)