Best way to run effects in stereo when using two amps is to process both H9 channels in a similar manner. Usually we have two options:
1-running each H9 output to its own amp input. 2-connect each channel of the H9 to each amp’s FX loop.
If you have two of the same amp, you may consider plugging into one preamp section and sending that signal to the IN 1 of the H9 and taking H9 Out 1 to Amp1 FX Return and H9 Out2 to Amp2 FX Return.
Any other way and you’re compromising the stereo image. From the title of your post, it sounds almost like you’re trying to run a WET/DRY rig, which the H9 can do, but it’s mono outputs for both signals. If you want to run effects in true stereo, it’ll have to be a WET/DRY/WET rig with three amps. This will also involve using signal splitters.