The process is very simple - create a directory on your PC, and in that directory place the files you want in the ROM mirroring the structure of the phone. So if you want /data/app/blah.apk in the ROM, create that directory structure and put the file there. When you have added all the files you need, ZIP the contents of the directory, ensure the ZIP is less than 10MB (it will be rejected if it is not) and then select it at the appropriate point in the online kitchen process.
This is a simple first version of this functionality, and going forward it will be possible to retrieve past uploaded zips by ID, share your uploaded zips with others to include in their kitchen builds and even upload or include multiple zips. It's a first step because you - dear members - said you wanted it.
Enjoy... and feedback is much appreciated!