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Please include sample messages for all sensor inputs, as well as the config for your _odom_ frame EKF. Without those, I can't comment fully.

Without that information, I have other questions and comments.

• When you turn on publish_tf for the second EKF instance, are you making sure to disable tf publication in whatever node is doing the fiducials? You can't have two nodes trying to publish the same transform.
• You are correct in your statement: first, you are fusing two absolute source of pose data, which is not advised, unless both are in agreement (think of, e.g., two GPS sensors), and moreover, you are using the EKF's own transform to transform data that it is trying to fuse. That's not really a huge deal, since the EKF uses its own state internally to do some transforms, but it will make your life more complicated. Any reason not to just fuse the velocity data from the wheel odometry? That's a common practice.