^What they said. You always have to continually edit your patches to suit wherever you're at, be it in the studio, at home or at a gig. It might be tedious, but that's part and parcel of owning an 'all-in-one'. The Pod basically simulates an amp, hence as long as you place your pedals before the Pod between it and your guitar they'll sound fine. That's if you're going thru PA. Pedals straight into PA sound terrible IMHO. You'd want them to be going thru an amp. Of course, if you're going thru an amp then where your pedals are in your signal chain depends on you. Experiment and find out what suits you.
I find the X3 impressive because now we can go into PA without DI, the ability to plug in both guitar and bass into the same thing and the thicker sounding amp and pedal models. However, the bass and guitar into 1 thing means that the soundman can only adjust the sound of both from the mixer, not just 1. Not sure if the X3 has a seperate output for bass y'see. I have only used it for little more than 5mins, but i was already impressed. The rest of the my opinions come from hearing it being used.