If you want to record some clean guitar, and then play it through the axe-fx, you will need some impedence matching equipment as linked to make the line-out from your computer/Edirol act like a guitar. Otherwise if you make all your patches for the line level signal, then you plug your guitar straight in, it could sound quite different.
EDIT: having said that, I put line-outs into my pedals all the time, no problem, it's just I wouldn't shape my live sounds based on that.