you want to run all your distortions and wah before your a/b/y/ box so that they will effect both your amps simultaneously. If you want to effect only one amp then run them after.
Mine Goes:
Guitar> Tuner>Whammy> Wah> Tremelo> Phaser>Sparkle Drive Full Drive> Rat > OCD > Noise Suppressor > A/B/Y > Marshall JCM 800/ Vox AC30
Marshall FX Loop:
DD3> Axle Grease> Chorus> Rotary> Reverb
Here are a few demo's
http://www.youtube.com/watch?v=Iyy6w77o2Ds
http://www.youtube.com/watch?v=hwpC_77L … re=related
http://www.youtube.com/watch?v=4EBPkVTB … re=related
http://www.youtube.com/watch?v=MfQIayNm … re=related
http://www.youtube.com/watch?v=hy5b2Gky … re=related
Amps: Marshall JCM 800, Marshall 1987 X Plexi, Vox AC-30, Ceriaton ODS HRM, Fender Bassman
Guitars: Gibson Les Paul's(Standard, Classic, and Studio)Es 125 T, Fender Strats, Telies, Wasburn Idol Pro
FX's: BOSS TU-2, Ibanez TS-808, TS-9, Dunlap 535Q Cry Baby, Fulltone OCD, Full drive 2, Supa Trem, Rat, Whirlwind Phaser, MXR Micro Chorus, Digatech Whammy, Line 6 DL4, Holly grail 2,Wampler Ego,Pinical