During the time of the poop-farts, I'd put a rag inside the diaper and just change that. I'd also, since I use the origami fold with a flat, sometimes just refold the middle section so the poop was on the inside and not against her skin.
We're at 14 weeks now and still have a poop-fart occasionally, but I think they stopped coming as frequently around 10-11 weeks or so.
Oh, and I'm sure you've already figured this out, but just in case...try offering the potty after a poop fart, often you can get your LO to at least put out a few more or even do a big poop and then you don't have to deal with as many poop-farts.