it should just treat it as a normal file. Are you getting an error? Does the upload start, then fail halfway through? Or does it fail outright? Anything in the logs? What kind of server are you trying to upload to?
If there is something actively preventing you from uploading zip files, one option is to change/mangle the extension before uploading. When it is uploaded, restore the extension.
If something is preventing the upload based on size, you may have to break the file up.