Actually, ZAppLink will work perfectly well with any UV mapping -- especially a distortion-free method like AUVTiles or GUVTiles.
That's the beauty of the plugin: There's no reason anymore to work with an unwrapped view of the texture. You use Projection Master to drop the model to the canvas, and then at any time you can use ZAppLink to send the canvas (not the texture) to Photoshop (or your PSD-capable image editor). There, you can use all the things that Photoshop is best at such as adding text, doing layer effects or applying filters. When you save that document and return to ZBrush, the entire canvas will be updated with the changes made in Photoshop. You can also keep working on the canvas with ZBrush's tools and features to do all the things that ZBrush is best at. Whenever you're done, pick the model back up again and continue work like normal.
You can finally be rid of the bad old days when you had to paint on the unwrapped texture and try to manually correct for UV distortions and texture seams. Paint what you want to see, all the time, and let the computer deal with that stuff for you behind the scenes. It's a much more efficient way to work.
Of course, ZAppLink is useful for more than just texturing. Since you're sending the canvas to your image editor, that means that you can use the plugin to do whole new things in your illustrations, as well.
my guess edonkey is that it uses grab doc to create a texture to send to the program then updates the canvas. i think it would need to do this or something similar because your model is dropped in pm. then you pick it up and the changes you made will be applied to your texture. something like that anyways.
edonkey, aurick can correct me if i'm wrong on this but, the work you do in photoshop via ZAppLink will only affect color information and will ignore the embedded materials.
You can actually get a feel for what zapplink will be like right now with the current zbrush. here's what to do:
get an object on the canvas in edit mode
change your material to flat shader
load up Projection Master (make sure colors is selected, and choose fade if you want)
while in Projection Master, save your canvas document as a .psd
open up photoshop or your psd-capable graphic editor and load the saved canvas document
begin to edit the image; paint on the model. When you're done, save the .psd
switch back to zbrush. Make sure your material is flat shader and select Document>Import and import the .psd
exit Projection master and examine your results
Start to experiment with this to get different results.
Tip: choose flat shader before entering PM and saving the .psd, otherwise when you import the photoshopped .psd and exit pm, the shading information that the zbrush rendering engine does will be applied to the texture as color information.
ZAppLink basically does all the exporting and material applying for your through a dialogue box so you don't have to. It also has some other goodies too though.