Yes. If you have rebooting to payload enabled, and Hekate as reboot_payload.bin, simply reboot (and hold Vol- to disable autoboot if needed) and select sysNAND boot. If you don't have a sysNAND boot entry, you can make one.
Keep in mind you are still in CFW and Nintendo could possibly detect this kind of CFW use in the future so I always suggest to boot sysNAND from normal boot rather than from CFW as it's more ban proof.
Atmosphere replaces the Restart function from the Power menu with reboot to payload so if Hekate is your reboot to payload, you can reboot into Hekate while in CFW.