The way I do it is to run the H90 in dual routing mode and go into the H90 input 1 > HX stomp input. Then use the HX stomp FX send > H90 input 3/4, then H90 output 3/4 > HX Stomp FX return.
You can then use the H90 routing options to either have both effects on H90 path 1 (both effects before the HX stomp amp), 1 effect on H90 Path 1 and another on Path 2 ( 1 effect before the HX stomp Amp and after the amp using the FX Loop), or have both effects on H90 path 2 (and have both effects after the HX stomp amp in the effects loop). It’s a really flexible approach!