When you delete a folder, the folder will be deleted only, your document activities will be still available in the activity archive of SuperOffice.
You will be only deleting the template, if the predefined template is used on projects, your folder structure will still be in place.
No, it will be only visible on the project you are currently working on, if you need this folder in the future on other projects, add the folder in the predefined template.
No, you have to use a predefined template, or create the folders manually.
The activity or document is moved based on the document or activity type, check your predefined template and make sure the document and activity type is connected to the right folder.
If documents or activities are placed in the root, it means that the document or activity type has not been configured to the right folder, this can be done in the configuration where you setup the predefined templates.