Layers are different than Channels. You may only have one Layer, but you will have at least 4 Channels -- RGB, Red, Green and Blue. Adding the Alpha will bring your Channel total to 5. If you have the Alpha hidden, you will get the "too many Channels" error. All of the Channels need to be visible. To quote the section of Sinastra's tutorial that deals with the Channels...
Select the Alpha Layer it creates, and paste your clipboard (the black and white image) into this channel.
Now, click and make all the channels visable (click the empty boxes next to them where you see the eye on the alpha mask).
Remember this step, it is a quick and easy way to do alpha masks!
Now save the duplicated image as a DDS file with the following settings: DXT5 ARGB 8 bpp | interpolated alpha