Hiya.
A6's WAD file format is a bit different from the 'normal' WAD format in that A6's can support high-color textuers (re: textures with more than 256 colors). If the WAD in question doesn't have any high-color textures, then, IIRC, Wally *should* open it. The QuArK mapping/editing program will do likewise. However, if the WAD happens to have even one texture that is high-color (ex: the "standard.wad" for A6), then other .wad programs will choke.
Personally, I'd use either Wally or QuArK to do extractions that are more than a handfull of textures from a wad. But if the wad is one with high-color textures in it...I think WED is your only option.