1. You can use ctrl+alt+[ or ] . This will move up or down in the stack of paths.
2. As I know the difference is that you can edit the effects after you apply them using the appearance pallette. The effects will appear stacked there.. and you can edit, delete or duplicate them. The filters are definitive (the way they are in photoshop) they’re not editable after applying and you can get rid of them only by using undo.
3. You can set the accuracy of the arrow keys in Preferences/General/Keyboard Increment. If you press shift while moving an object with the arrow keys, the object will move with 10 x the increment set in the preferences.
HTH