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I suggest to keep a tile as simple as possible, like you do with only giving it an ID, perhaps a bool for collision or any other simple things to identify what type of tile this represents. A class like this should look like, (All pseudo code, i'm a C# guy but implementing this in java should be a breeze if you know the basics):

class Tile
{
    public int baseID;
    public bool Collision;
}

This is pretty much all you need to draw everything necessary and have collision working. You just build layers of these in this order from back to front from left to right from top to bottom. (It does not need to be in this order if every sprite fits within the tilesize.)

Tile[,] baseMap = new Tile[100,100]; //Put in all your backgrounds
Tile[,] objectLayer = new Tile[100,100]; //Put in all your objects
Tile[,] anotherObjectLayer = new Tile[100,100]; //Put more objects in a separate layer.

You would draw it like this:

for (int y = 0; y < mapheight; y++)
{
    for (int x = 0; x < mapwidth; x++)
    {
        draw(baseMap[x,y]); //Obviously you need your implementation of ID to texture here.
        draw(objectLayer[x,y]);
        draw(anotherObjectLayer[x,y]);
//Drawing it like this will result higher/further tiles to be covered by larger objects like tree's. 
//You need to find out where the moving things are, like the player, to draw them on the correct [x,y] iteration.
    }
}

If you need slightly different variables and parameters for a layer you are free to create another class for these. Maybe inheriting from the base tile class will do you good. Here is an example for a chest tile:

class Chest : Tile
{
    //The baseID would be it's texture.
    //The Collision can be used to have hidden chest or burred treasure.
    int ChestItemID; //The item ID this chest holds.
}

Since this class inherits from tile it is perfectly fine to put this in one of the above layers so you do not have to create a complete layer arrays just for chests.