The mode toggle is quite effective. With a shift button I assume you had to hold it down? It's probably easier (depending on the button you want to press) to hit 2 buttons in succession than it is to hold one, click another, then release the first.
One or two times I've noticed when I switch modes too fast that there might be a little "mode switch" lag.
I had a button mapped to "WEP" in mode 2 and "Combat Trim toggle" in mode 1. So if I hit mode2-WEP-Mode1 too fast sometimes it would toggle CT instead of WEP. That's only in extreme cases, mind you, where I'm really getting hyper about it. I could have just fat-fingered it. I suspect it's an issue with the internal chips inside the stick rather than in the game itself.
You should be able to get the hang of it pretty fast.
My stick mapping for the Sidewinder was this:
MODE 1:
Handle:
Trigger: fire primary
left side oblong thumb button: fire secondary
Upper right thumb button: Secondary select (bombs, rkts, etc)
Lower right thumb button: Combat trim toggle (hit it once, turn it off)
Hat: As normal but I mapped "forward" to be "Forward-up" by default. Some map this to a moved-in or zoomed-in position for better aiming.
Base: I have 4 buttons offset from the throttle and then the shift button at the back.
Shift: Zoom toggle, thumb normally resting on throttle
Left Near: Mode 2 toggle
Left Far: Flaps down
Right far: Flaps up
Right near: varried, sometimes did damage toggle, sometimes gear.
MODE 2:
Handle:
Trigger: fire primary (when you gotta fire, you gotta fire, no matter what mode you're in)
left side oblong thumb button: fire secondary (same reason as above)
Upper right thumb button: varried, sometimes chat buffer toggle, sometimes zoom toggle)
Lower right thumb button: WEP toggle
Hat: Same as Mode1 (basic combat functions the same with views/triggers, I use the modes for extra buttons)
Base:
Shift: Zoom toggle, thumb normally resting on throttle
Left Near: Mode 1 toggle
Left Far: brakes
Right far: gear (if not already mapped in mode1) or bomb bay toggle
Right near: varried.
Sometimes I used right far and right rear in mode2 for elevator trim up and down. Most times I forgot about it