Sure airmess.
I had the same problems to go through, and then ran across Machnix post about transparency.
Thanks to that, the "1" marking and the shield part is practically invisible, without any ugly traces of it on the skin.
.........
I'm assuming that you use Photoshop.
1. Cover up the part which you want to be transparent with a certain color that you're sure its not gonna be used by some other part - like deep purple.
2. In the case of the E-4, the "1" and the Schlageter emblem overlaps the fuselage skin - so, you want these to be transparent. Patch it up with the 'transparency color' of your choice.
3. Then, after you finish the skin, convert it to indexed colors.
4. Then, open the "info" window, and move your cursor over your transparency color - among the info, you can see a "indexed" value of the transparency color.
5. After producing the BMP files, create a file named "_a.txt" inside your skin folder where the BMP files are placed - in the case of the E-4, it would be "109E41_a.txt".
6. Write down the indexed value of your transparency color, and save the txt file.
Then whatever part you patched up with the transparency color, will show up as totally transparent!
Pretty neato way of cleaning skins out.