There are two considerations with large packages...
First, be aware that there is an artificial cap on package size at 384mb. We have a utility that can be used to increase that limit, if you've not already done so.
Second, where large packages are concerned and you're still working out details on rules.. I would suggest publishing the updates as Metadata Only updates until you get the applicability results you expect, and then you can republish Metadata Only revisions without having to upload the binaries. One note on this -- it requires a hotfix which is included in KB2720211 or KB2734608, so make sure one of those updates is applied to your WSUS server.
Once you've finalized the metadata, then you can do a Full Publish including the binaries.
There's also a Content Type called "Revision Only" which should upload only the metadata, not the binaries, but I've not personally used that Content Type in publishing.
Thanks, I'll give that a try
As an aside, it looks like Patch Manager doesn't consider the additional files when calculating the package size. I haven't implemented the utility to increase the size limit, but I am still able to upload my 1.5GB package, though it takes forever. Also, in the package details view, PM shows that the package size is only 52KB, the size of the executable