The Boss FS-6 is not a switch we have tested, but from reading the manual, it is possible to change the polarity of the switches from Normally Closed (NC), which is the Boss standard, to Normally Open (NO), which tends to work for most non-Boss pedals. Also, the switches should be set for momentary operation, not latched.
Just to confirm, I have a pair of FS-6s I use with everything – including the H90 – set up exactly as Joe described above. The LEDs are kind of useful to indicate which modes you’ve set the little slide switch options to.