The same process is how every other EU wide regulation goes into effect. EU passes it, the member states get their input during the EU process, and the member states are then obligated to abide by the rules.
An analogous process, which is not a perfect analog but is similar, is how US federal rules get passed down to the states. The states get their input on federal legislation at the federal level, but then must abide by the resulting federal law.
I'd also add that giving every country a veto on any legislation would basically guarantee nothing gets done.