I dont have a Ipod, i have a ZVM. However, i have the BSE on it right now. After a few days any little bubbles will make their way out. As long as you pushed the bubble to the closest corner/edge you should be ok.
Now, i removed my BSE off my touch for 1 reason. IT SUCKS when you fingers are wet...not even wet, when you hands are clammy or you grab a nice cold drink, if you touch the BSE, your fingers will kinda skip on the skin. It almost feels tacky. I wouldnt use the click wheel part unless you ready to deal with that.
Just my personal opinion, people on the ZVM forums voted on how many people actually use the skin on the touch pad, i think it was like 85% of people dont use it for the reason mention above.
Again, totally up to you.