Attaching an alpha channel

So I have a couple of clips uploaded to which I would like to attach alpha channels. Since they're Photo-JPEG I have to export the alpha separately.

P5 gives instructions on how to attach an alpha channel to it's RGB clip using the FTP client upload method. However, I use the new Java uploader to upload my clips.

I emailed P5 about this, but it's been over a week and they haven't responded. Does anybody know how to attach an alpha matte clip to it's RGB clip if you're not using the FTP upload method?

A long time ago I used this method - you just combine both files into the one with After Effects or MpegStreamclip or any other software.
BUT Pond5 prefers to have the files with alpha in PNG+ or Animation codecs. So, all my new files are in PNG+.
Zygis

Ok. The way they worded it on their video requirements desription made it seem like they wanted Photo-JPEG Quicktime .mov whenever possible.

@kgries3

The following is from the video guidelines:

Animation or PNG: ONLY for clips with embedded alpha channels.

What you are thinking of is alpha matte which some use on other sites which do not except embedded alpha clips.

Alpha mattes are not ready to use but embedded alpha channel are when downloaded.

Yeah, I understand that. Thanks.