Search how to properly caulk a crack such as an expansion joint.
You stuff the joint with "backer rod" and then caulk. Backer Rod is a closed cell foam "rope" or tube. Comes in many sizes from about a 1/4" up to well over an Inch. Home Depot carries it locally among many other sources.
The "trick" for you would be to stuff it into the crack without pushing it out fo the bottom. Then, the caulk should be thin at the center of the joint and thick on the ends where it touches the decking. The idea is that its thin and flexible and stretchy at the center and wide or thick where it adheres tot eh deck board. the cross section is shaped like a bowtie. The thin center can stretch and flex and the wide contact on the deck boards allows for strong adhesion.
Can't imagine filling a joint every 6" and getting them all done well.