Stefan, Not a stupid question at all!
But I do not quite understand. First let me explain a little. You may aredy understand the following but I have included it just in case.
As you probably know the basic structure of jD are that files are stored in directories together with a database. A Download consists of various items of information in the database such as the Download Name, the file name, descriptions, price, images and so on, and of course the downloadable file. A Category is a directory and also some information and details stored in the database.
The monitoring system always looks at all the directories and files from the root directory, normally called jdownloads and situated in the Joomla! root diectory. If it finds a directory in the tree that does not have a matching Category entry in the database then it will create one. Similarly if it finds a file in a directory that does not have a corresponding Download in the database then it creates a new Download.
Quite often when there are a lot of files to upload this is done by using an ftp program such as FileZilla. However before doing that I would recommend that the jD Config - Monitoring tab field 'Download Directory Monitoring?" is set to No. This is to avoid a 'race' condition where you are part way through uploading and an auto monitoring sequence is triggered by some other event. Whilst looking at the Monitoring tab also check out the other fields.So when you have uploaded the relevant directories and files one goes to the jD Control panel and clicks on 'Check Download Area now'. This is in the Status tab of the control panel.
What I do not understand is when you say
When I activate "Check Download area now." or "automonitorin" I get a lot of unwanted downloads and categories.
Why have those directories and files been placed in the jD 'tree' if you do not want them?
If they are truely unwanted then you need to use jD to remove them. If you delete them directly you will leave a mess in the database. First use Dowloads page to delete the actual Download entries. Also before deleting check the settings of jD Config - Downloads tab - fields 'Delete images from deleted Downloads?' and 'Delete preview files from any deleted Download?'.Often the easiest route is to filter the Categories concerned in the Downloads page. Then you can delete the relevant Category.
However this might not be what you mean. If I have misunderstood could you please explain a little further pleaseColin