I recommend you to use The All-Seeing Eye to start Enemy Territory, since I think it's alot handier than just running ET.exe (I use some plugin program's).
Anyway here's how to do it manually:

You have got 2 executable files:
- sleep.exe
- patch.exe

For the manual function, you only need to use patch.exe. Selecting the patch for Enemy Territory is a piece of cake. Just run the patch.exe and select the patch you want to use and click on "Patch". Now you're finished and are able to start ET.exe at the patch you selected.

If you want to use the other patch do the same sequence again.