Here's what I'm thinking:
1) Display a screen that asks for the order number. (You'll need this on the RPG side before displaying the upload widget.) Maybe you already have this.
2) RPG program calculates the upload directory from the order number, and puts it in a field.
3) field from #2 is bound to the "Upload Directory" on a File Upload widget.
4) File Upload widget takes care of uploading the files to the IFS.
In order to use the file upload, you need to define an "exit program" on the server. This is really simple to write, just a simple RPG.. It's explained here:
http://www.profoundlogic.com/docs/display/PUI/Security
That exit program can create the directory if it doesn't exist (this would be just extra code in the exit program). Or it could be done in step #2 by your RPG program. Either way would work. (Though, I like the exit program idea, in case the user hits the "cancel" button and doesn't upload anything The exit progam isn't run until the file is uploaded, so it won't be run if the user cancels)
Creating the directory can be done with the CRTDIR CL command, or with the mkdir() IFS API. I can provide an example if that's useful to you.
One more thing: If you upload to the /www/YOUR-PUI-INSTANCE/htdocs/profoundui/userdata directory, you should be aware that this directory is addressable by a direct URL, such as
http://YOUR-SYSTEM:8080/profoundui/something.something
This may be a security issue, because users can bypass your application to view what's in those directories (if they know the URL). So it might be prudent to store in a different IFS directory, such as /your-app-name/data or something, outside of the /www part of the IFS.
The trouble with that is you wouldn't be able to get at the data once you put it there (at least, not via HTTP). So it's secure, but then when you need it, you can't get it. The workaround would be to write a program that downloads the data, but imposes security checks...
I know I'm throwing a lot of stuff out at you, and not going into much depth on it... please let me know if I can help further.