To my understanding, you're handling the stress boxes correctly. As an example, if you took some hits in combat as a giant:
OOOXXO(OXXO)
Then, if you shifted back to human, you would have:
OOOX(OX)
If you then took a four stress hit, it would roll up into your Toughness track:
OOOX(XX)
And if you turned back into a giant you'd still have some bonus boxes marked off, assuming you hadn't had time to recover:
OOOXXO(XXXO)
Then, if you took a seven-stress hit from FIRE, it would ignore that last unchecked box completely, taking you out (unless you took a consequence).
Conceptually, it might help to draw a box around boxes 5-6 and 9-10, and just pretend they don't exist unless you're shapechanged.
The value of the Catch does track with what I see in the book. One thing, however, is that my understanding of 'Human Form' is that you are supposed to be basically mundane when in human form. Which means that you shouldn't have any strength, recovery, or toughness at all in that form. The rules are a bit loose on this, stating that you must "Specify which of your supernatural abilities (usually most or all of them) are unavailable", so you've got the wiggle room so long as your GM OKs is, but consider that your 'average Joe' human form will be *very* inhumanly powerful (literally), enough to compete physically with many monsters, which is something of a stretch.