In map properties of the base map, you'll find a note box in the bottom left of the window.
You can put the note tag <LAYERanynumber map_id> in that notebox. An example of what that notetag would look like using map 23:
<LAYER1 23>

So if my map is map is named lake1 and the bridge is called layer2 how would i write it. i dont quite understand why the layer can be any number .

Becuase you can layer more then one map on another, the anynumber determines the order, with layers with larger numbers being drawn first and so on. The names of the maps have no bearing on what you use for the notetags, two maps can have the same name! You have to use the map id. It's shown as a three digit number in the title bar of map properties, and in the status bar of the program on the bottom right for the map being currently edited (I have to tell a lot of people this, don't add the extra 0's. Even though it says 004, you do 4, 004 is not 4.)

Let's say your map named lake1 is id 1 and your map named bridge is id 3, you would put in the notebox of Map 1:
<LAYER1 3>

alright so i did that but visually i am not seeing a diffrence I wrote <Lake12 17> on the lake map properies and nothing visually changed and i double checeked the id numbers in the top of each map page.

As I said, the name of the maps have no effect on what you use for the note tags.
It's always LAYER.
So try <LAYER1 17>
(I notice in my previous example that the lake1 id and the layer number were the same, but they dont have to be, it can be any number between 0 and 999, just determines which layers are on top.)

I got what your last example meant My tag is set up as <Layer12 17> because i am trying to put map ID 17 over Map ID 12 but neither visually appear in the other.

Not Layer, LAYER. Has to be caps.

i had it like that And i think i got it working just gotta mess with the tile properties, thank you for the script, your paitence, help and time.

Woot! Glad it's working for you now~