Given that everything is up for grabs now, how would you prefer it?
Both Jonathan and Martha die before Clark becomes Superman: Basically the Pre-COIE and New 52 version. Either they die naturally, in a car accident or they can retain the part where Vyndkytv had something to do with their deaths.
Jonathan died pre-Superman, Martha lived longer but eventually died: Something akin to the Donnerverse Superman movies. This allows Martha to have been around to see her son become a world-renowned hero, meet his future wife, possibly even meet her grandchild.
Jonathan and Martha both lived to see Superman, both eventually died: Basically, the Post-COIE status of the Kents living to see Clark becoming Superman remained - except that they both eventually died, which may or may not have been before Jon was born.
Jonathan and Martha both lived to see Superman, Jonathan eventually died, Martha's alive: Picking up directly from the pre-Flashpoint status quo. It also means that Martha has miraculously returned to life and will be a presence in the books moving forward!
Jonathan died pre-Superman, Martha lives: This is currently the status quo in the DCEU. It retcons pre-Flashpoint, but leaves Martha alive to remain a presence moving forward.
Jonathan and Martha both live: The predominant pre-Flashpoint status restored fully. It means both Ma and Pa Kent remain a presence in the books moving forward.
Martha is dead, Jonathan is alive: Subsuming all the variations of this unprecedented move into one option. Its something that hasn't been tried before and I don't specifically see the merit in it but its worth considering for the sake of completion.