Yes, this would be the correct way to do it.
If you have your guitar on input 1 and your synth on input 2, the H90 will think that is a stereo input and you will most likely have undesirable results with how the effects processing works.
Guitar on input 1 and synth on input 3 will give you the correct mono inputs, use routing mode to determine where the synth (insert 1) is in the signal path.
Let me know if you need any help with this.