(a) There is currently no option to universally turn cabs/amps off. So you best bet is to either create two sets of patches OR include them in each patch with a footswitch to turn them on/off. (that'll soak one of your footswitches though. (b) As to how to run to your amp, you plug your guitar into your helix, then plug the "1/4 inch output L(Mono)" output to your amps guitar in. This will perfectly simulate a pedalboard going into the front of your amp. If you would rather use the effects loop of your amp, same deal you're just going FX send -> helix -> fx return.
© As to effects, if you just get a blank preset and plug the helix in as described above, you should just be getting the sound of your amp without any toneloss/change. Then you can start adding blocks as you'd like, and assigning them to footswitches by holding your finger on them for a couple of seconds then selecting "assign". Anything else we can help with?