I am always happy to use up and give a cert to the GA. I have it in my hand ready to turn in whether it is asked for or not.

If not using online checkin, the checkin agents usually staple the cert to the back of boarding pass (not always). Also, write some notation by hand in addition to the pre-printed CERT notation on the BP.

Cert is usually collected at the gate. However, IIRC, in some cases (HKG and LAS) certs were taken at checkin counter. (I usually request that a note is made that the cert has been lifted/taken at checkin.)