Hello, you have to follow the instructions of the accessory you've purchased. If it's to be installed on the roof line with included clips, then that's what you do. But I don't know of any time or any manufacturer that suggests modifying weather strips.
RepairPal Certified shops can diagnose and repair your 2014 Chevrolet Equinox. They provide transparent pricing with a minimum 12-month or 12,000-mile warranty on repairs and services.