Best way to set up a song?

There is a Wah seting that automatically turns it off when you are not using it. Take your foot off the wah, and switch on the rotovibe. At the end of the song, switch off the roto, and start your wacka wacka foot movements again.

BTW - what tempo is this song? Assuming it is uptempo, you can make the switch 1/8 note or so before the end of the measure, and your change will sound instantaneous and effective on the downbeat.

If you wanted to switch many effects at once, without changing rigs, there is a "Stomps Invert" function that turns all active effects off, and all inactive effects on, using a single button push. I think it may include post effects, too (check the manual).

When I have complex multi-effect changes, I use separate rigs. That is much simpler than planning/programming complicated rigs.

For rig editing/saving/renaming practice:

Pick a rig you DON'T like -
Change something in it -
Press the "Store" button -

You'll get the option to "replace" the rig (this is not what you want to do), or save it as a new rig. You will be able to rename the new rig.

Why don't you use the performance mode for this song?
I use one performance per song. The performance will be named as the song. You have five slots per performance. I use one Rig per song but with different settings within the slots. For example you can use the slots for Intro, Verse, Ref, Bridge and Solo and store the same Rig for Ref as for Verse but switch off the delay, increase gain and switch on chorus. You can adjust the levels for each slot also. During performing the song you need one footstep only.
This ist the best way for me to use the Kemper.

Yes, exactly.

Yes! Performance Mode is a very cool feature. For each slot you can change everything (amp, cabinet, level, effects...).

To clarify, the performance won't remember your edits unless you save them before switching to a different rig or performance

You can also change settings in a rig you like. If you dont want to overwrite, push the store soft knob and than the soft knob for "store as". Name it like you want, the old one is still in your kpa.

You can also export a Performance Slot back into the Browse Pool, say if you've made some changes to it during the gig and you want to save that as a new rig. Very handy I think.

Yes, its also a very nice feature, called store to pool in rig menue.