Yes, SafeSky will still transmit your position to its servers — but in your setup, the GPS position will come from the SkyEcho 2, not your mobile device.
Even though SkyEcho is used only for ADS-B IN (receiving traffic), once it’s connected to SafeSky, it becomes the master source for GPS data. SafeSky will then transmit your position to its servers using the GPS data from the SkyEcho, sent via the mobile phone’s internet connection.
Since you’ve correctly configured the same Mode-S hex code in both SafeSky and the SkyEcho, you’ll avoid the “double echo” issue — so you’re all set for proper integration.