2 Q's, door overlay/decals and custom overlays/decals

Question 1:
How does one properly display the metal door decals? For instance, if you go to B from BLU spawn on gravel and go left, there's a metal door at the end of the tunnel in front of you. When I try to use them in a map, they still have that black background pictured on them. Also, I applied this as an overlay.

Question 2:
So I got 2 custom textures loaded fine and display correctly in game, however I could not get them to be added into the BSP. I tried valves BSPZIP but I keep getting "could not find directory" errors when they all exist and I tried pakrat.
Steps I followed for pakrat:
1. Load my_map.bsp
2. Clicked "Add" and selected Texture1.vtf/.vmt and Texture2.vtf/.vmt
3. Then I clicked File->Save BSP and overwrote my_map.bsp
4. I analyzed the file my_map.bsp and it said Texture1 and 2 were not added

Am I doing something wrong with pakrat? Does it not work with TF2?
*note: the custom textures I am using I want to use as overlays in case I'm doing the .vmt files wrong

If you need any other info let me know. Thanks.

It was set to:

"LightmappedGeneric"
{
"$BaseTexture" "materials\maps\my_map\Texture1.vtf"
}

Thanks for the help. I ended up getting Z's packager and after messing with bspzip some more, I got it to work that way too.

Youme: Thanks for the info about those doors.

Update: I tried Z's packager, bspzip, and pakrat. According to all 3, my 3 vtf and 3 vmt files were added successfully. However, when I rename the materials folder and load my map to test it, the do not load and it's the pink/black texture. Any idea what'd be causing this?

If it's compiled and then I rename the materials folder, they aren't suppose to show up? Even though the textures are in the BSP file?

I got it working. Turns out it was another "stupid user" error. For got to change the path in my vmt's.