Your pictures are stored once, inside Pictures/ iPhoto Library, in folders based on the "rolls" created when you import into iPhoto. They are not duplicated where you see them listed in the Source Pane by year or by Albums you designate (topic?). Albums merely tell iPhoto which photos to display together; they do not duplicate your files. A photo can be in 10 albums or no album. To see your entire iPhoto library "inventory," that is, each photo once and only once, choose Library from the Source Pane.
To understand the structure of the iPhoto library, look at a diagram by lori_diloreto:
http://homepage.mac.com/loridilo/.Public/iPhoto6.jpg
Note from the diagrams that there are 2 or 3 versions of each file in the library. These are not duplicates, and each file is important. Your original, full-sized photos are stored inside the Originals folder. They will not be changed when you edit or export a photo; iPhoto always preserves them. Edited versions are stored in the Modified folder. They are linked to the original version so that you can always discard your edits and revert to the original version. This is the version control at the heart of iPhoto. Each file you import also has a small thumbnail version in the Data folder. The thumbnails are displayed when you view your library in iPhoto, which allows the application to run efficiently. In order for iPhoto's database to perform properly, you must Import into iPhoto, and always use iPhoto to access these files (never access them from the Finder!).
1) You can't stop it from creating a new roll, but you can go to View > Sort Photos > by Film Rolls and edit your rolls. To move photos to other rolls, select one or more pictures, then drag to the name of a roll until it becomes selected, then drop. Or select photos and use the menu to choose File > Create Film Roll to place those photos into their own roll. Any roll that becomes empty will automatically disappear. With a roll name selected, you can also change it's title, date, or comments by typing inside the info pane (lower left corner of iPhoto window). You can get your rolls organized however you want, as long as you do it from within iPhoto.
2) The years are automatic Smart Albums, which you can not turn off. They do not cause duplication in your library. They are just a short cut for finding your photos. If you don't want them listed in your Source Pane, click the little triangle beside the word Library. The triangle will point to the right, and the year albums will be out of view.
3) By "subject folders" I assume you are referring to the Albums that you create. A photo must be in your library in order to have it in an album. If you delete it from the library, it will be removed from all albums, slideshows, books, etc. The file is in your library once; your albums simply point to those files.
4) Adding photos into the Pictures folder does not import them into the iPhoto library. It is fine to place items in Pictures, as long as you stay out of the folder named iPhoto Library. You might have image files that you don't want saved in iPhoto for some reason. [I keep digital scrapbook pages, but I don't want them in iPhoto, for example.]
Saving files directly into the iPhoto library folder is not recommended, will not correctly import the file into iPhoto, and could cause damage to the library. Note the Golden Rule of iPhoto: Do not tamper with anything in the iPhoto library folder from inside the Finder.
Want to find your photos so you can upload to a website? You can select photos from inside iPhoto, File > Export > File Export to a desktop folder, choose that folder for uploading, and trash that folder when done. Or right-click on a photo's thumbnail and choose "Show File" from the contextual menu. A Finder window will open with the photo selected.
Apple has a nice iPhoto tutorial at
http://www.apple.com/ilife/tutorials/iphoto/
Please feel free to post back with further questions or if you'd like clarification on any of the above.