I don't really understand your problem.
You like to use FS1-4 as effect switch and FS 5-8 as toggle switch between amps. That is the normal way. Create patch A with the desired effects and amp model 1, then save it also as patch B and change the amp model. Same efx's different sounds.
Handicap: if you switch from patch A to B you will get the stored on/off mode for the efx's.
I sometimes use two amps in one patch and toggle them with the pedal in pan-mode. Advantage: you can mix two sounds, handicap limited memory. You can only use less efx's.
To toggle between clean/distortet sound, you can use the distortion modules within a clean amp model. Instead of toggle between A/B use pedal as pan between channel A without distortion and B with distortion.
Or another possibility: use the toeswitch of the pedal for on/off distortion.
So feel free to find your best way. I use them all.
BTW I guess there is a mode were you don't switch between bank A-D but use the switches as on/off switch for efx's. But I haven't the HD500 just around me and I am not quite sure how to do this. Just have a look in your manual.
But always keep in mind: Using 2 amp-models in one patch will limit your memory extremly!