Hello RDIAZ1992,
This really comes down to personal preference. Do you run the amp/cab models in the Tone X clean or do you use them for any type of breakup or distortion? If you run the amp clean and get most of your dirt from the Protein or H90, then you can just connect the H90 output directly into the Tone X. Run the H90 in the default Insert mode. If you want to explore more possibilities, then put the Protein in the insert of the H90 and you’ll be able to run an Eventide algorithm before or after your Protein, basically anywhere in the chain.
My personal preference with the Tone X is to run the H90 in Dual Routing mode so Path 1 can go into the front of the amp (Tone X). Take the output of the Tone X and use Path 2 on the H90 for Post effects, usually all time-based effects. If you experiment, you may prefer the sound of these effects after the amp model. On a program basis, you can decide if you have two Eventide presets before the amp, two after the amp, or 1 effect in Pre and the other effect in Post. I would place the Tuner, Volume pedal and Protein before Path 1 (IN/OUT 1) of the H90.