Hi people!
There seems to be some misunderstanding here.
First off, the Alpha Channel (not layer; it has nothing to do with a layer at all) is found in the Channels palette.
I have recently realized that some people think that the little black and white image that may be seen next to the thumbnail on the Layers palette is an Alpha.
It's not. It's a Layer Mask. They are two totally different things. Layer masks control transparency in Photoshop, but not in Second Life. SL will never, ever, read the Layer Mask to derive transparency for the image.
It doesn't matter what you do or don't see in the Layers palette, because the Alpha Channel is totally independent of the layers.
My tutorial assumes that you have built your image from scratch, working on transparent layers. But that is not the only way to work; there are dozens of ways to build up your texture. I can't know which one you are using.
As an example, say you wanted to have a picture of a rose, used as a tattoo, in SL.
You could open PS, choose a Brush, and paint your rose on a transparent layer. Or you could take a photograph of that rose tattoo you have, and remove everything but the rose.
The techniques are very different, and will have different results. In the second case, you have to do extra things to eliminate all vestige of your skin. I didn't mention them in my tutorial, but if you have any non-image colors in the Solidify "rainbow" you'll need to Undo the filter, remove them, and run it again.
I used the easy case, where there is nothing to begin with but the colors you want.
If that's what you have, then these steps will always get you a perfect "cut out" with no white borders.
1. Make a copy of the file. Always keep the Layered PS file. Among other things, it can prove authorship if your work is stolen, and you need to file a DMCA or something.
2. On the copy, Merge the Visible Layers. You should now have an image with the Checkerboard showing below it. If it's on white, you didn't Merge Visible, you Flattened. They aren't the same thing. Put L$20 in the pot in the middle of the board, and try again.
3. Hold down Command/Ctrl and click the thumbnail of your image in the Layers palette to select the filled pixels. You should have "crawling ants" around any part of your image that is more than 50% opaque.
4. Go to Select > Save Selection, and accept the defaults. This steps saves the selection as an Alpha Channel, in the Channels palette. That's why you're asked if you want to save it as a new *Channel*. You can go look in the Channels Palette to make sure it's there, if you want. Any part that was selected will look white, anything that wasn't will look black. Now that your Alpha *channel* is made, it doesn't matter what else you do to the image. The transparency is now fixed.
5. Drop the selection. You want to run the Flaming Pear filter on the whole thing, not just the selected part of your image. If you don't drop the selection, you'll have a white halo in SL. Put another L$20 in the pot, and try again.
6. Run the Flaming Pear filter. Your image should show a totally solid rainbow streaking out from your original design. NOTE: YOU CANNOT SEE THE TRANSPARENCY IN PS. But it's there, safely tucked away in the Alpha Channel.
7. Save the image as a 32 bit targa (.tga) file. That's 8 bits for each CHANNEL. Red, Blue, Green, and Alpha. 8x4=32. If there wasn't an Alpha channel, you would only need 24 bits, because 8X3=24.
8. Upload to SL. Look at your image in the Preview window, before you spend your L$10. You can use the very same keyboard shortcuts to zoom in on it that you do in SL. See the checkerboard? Good! Then your image is what it's supposed to be. Collect all the money from the Pot, and proceed with the upload.
Really, people, this is very simple.
I think that you're confusing yourselves by not understanding that Channels and Layers are two totally different things that operate independently. And the reason you're not, I'm guessing, is that you've never really played with the Channels palette, and don't fully grasp what a Channel is.
So try this; split the Channels palette off from the Layers palette, so you can see them both at the same time. Now, as you make layers visible and invisible, watch what happens.
You'll find that no matter how many layers you make, you're still seeing only the RGB (which is a combination of the three channels directly below it,) the Red, Green, Blue and any Alpha you might have.
The number doesn't change. But what you see in the thumbnails does.
The RGB will always show your entire image, just the way you see it on your screen. That's because it's a combination of the brightness in the Red, Blue and Green channels. Essentially, those three channels are telling your computer how much of each of the three primary colors of light (Red, Blue, and Green) to pump into each pixel of your image.
Now, go to your Photoshop Preferences General pane, and uncheck Show Channels in Color, if it's checked. You'll see that the thumbnails in the Channels palette now show as black and white images. White is where a pixel is pumped up to 255 (as high as the eight bits can go. It's all a scale of 0-255, for 256 possible levels of each primary color of light.) Black is where there is none of that color. And all the gray shades, of course, are where the levels of the color are in between.
You might already be familiar with this, if you are used to choosing RGB colors as, say, R 216, G 154, B 123. Now you can see it, in levels of gray, in the palette.
If you click on the name of any of the channels, you'll see just that channel in your main "picture" window. It will look like a black and white image, and will probably surprise you with the values it's showing.
Click the eyeball next to any two channels to turn them both on, and you'll get a very oddly colored image that uses the data from those two, but ignores the third channel. You'll find that white things look yellow with just Red and Green, cyan with just Green and Blue, and magenta with just Red and Blue. That's the secondary colors of Light, in action.
When you've played with that long enough to familiarize yourself, add an alpha channel, using the method described above.
You'll notice that it pops into existence as soon as you Save Selection. You can click on its name to see it in isolation (start from full color, or RGB, not from a two color combination to do this.) You can combine it with any of the others, or all of the others. It'll show as a red tint, like an ancient rubylith, if that means anything to you.

But that's the only way that you can directly see your Alpha. Why, I hear you asking, doesn't PS just show it as transparent?
Because that's not all that an alpha can be used for. You can use them to save selections, to make complex selections, to hold information about spot colors, and all kinds of things. SL interprets them as transparency, but that's not their sole purpose. So it would be very confusing to show them as transparency for everyone who is using them for something else.
Okay, when you've done all this, you'll know that a Channel is a Channel, and a Layer is a Layer, and they aren't the same thing at all.
Hopefully, that will totally demystify the whole "Alpha Channel" thing, and you'll realize it's just another channel. But instead of driving one of the primary colors of light, it drives the transparency in SL. Other than that, though, it works exactly the same way.
White is pumping the pixel to full opacity. Black is leaving it totally empty, or clear. And the 254 shades of gray are putting one of the 254 possible levels of partial opacity into that particular pixel of the image.
Hope this helps!