You would only be able to post to one substeem. The tags would work like they do now. They just tag.

For example, you might post to /s/photography and tag travel. Or you might post to /s/travel and tag photography.

In the first example, the substeem is photography and those rules apply. The tag of travel has nothing to do with the substeem, it's just a tag. But I can certainly see how this might be confusing.