No.
They are only there against attacks that don't involve the Catch. So if I hit a guy with a stress track like this:
OOOO(OO)
for five stress without using the Catch, his stress track looks like this:
OOOO(XO).
If I hit him for five stress with the Catch, then the hit ignores those two stress boxes and takes the guy out.
Does that make sense?