how do i get each of those to come out a seperate output?
When the H90 is connected in stereo, the algorithms cannot be force panned to either side. For what you want to do, Dual Routing Mode is the best option.
Is the only way to have seperate effects to seperate amps to use dual mode?
Yes. However, there are some algorithms that automatically pan effects to left and right specifically, but it depends on the effect. Rotary is not one of those effects.
If so how do you make dual mode out 1 and 2 instead of 1+2 and 3+4?
Not possible. Because Dual Routing Mode allows mono and stereo paths depending on whether or not devices are connected using one or two outputs, it always requires four outputs be available, two for A, two for B.