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>Is there a way to avoid creating a 720 540 PSD and then crunching
>down to 486? And somehow keep circles circles and photographs not
Not really and then "crunching down" is very much a matter of point of view. The real question is: Can you accept the variations e.g. in antialiasing introduced by creating your work with non-square pixels in Photoshop. Apparently doing so will affect horizontal sampling more than vertical and as there is a difference in how AE and PS deal with these matters, the result would be different. It also extends to the matter of how practical it would be to work with such files if you need to move them to applications that don't provide PAR correction...
>Why does the DV viewing mode in Photoshop effect the importing into
>After Effects if it's just for preview purposes?
It doesn't. The people told you only half the facts. Photoshop's PAR correction is just for viewing purposes, that's true, but it does not mean that PS itself would be unable to deal with non-square pixels. Whenever you create a files based on such presets, PS will correctly embed that information for saving, hence programs like AE that are able to extract that information, will use it to correctly interpret items.
>How do you import an illustrattor file into After Effectcs with
You can't. In the strict sense Illustrator has no layers, only objects and groups and since they can be infinitely combined in the funniest ways, it's a hell of a thing to read them right. Maybe in CS5 after all these years... (or even later).
I'll answer the easiest question (#3) first:
When you're importing an Illustrator (.ai) file, are you choosing Composition (or Composition - Cropped Layers) from the Import As menu in the Import File dialog box? Or are you leaving the setting at the default of Footage? (See "Import a still-image sequence as a composition".)
If choosing one of the Composition options isn't working for you, then this we'll have some troubleshooting to do.
Regarding question #3:
You can import an Illustrator (.ai) file with separate layers. Just make sure that you have Composition (or Composition - Cropped Layers) selected in the Import As menu in the Import File dialog box. If you instead have the default Footage option selected, then all of the layers get merged together.
(See the "Import a single still image or a still-image sequence" section of After Effects Help on the Web.)
If choosing Composition from the Import As menu doesn't work for you, let us know.
I think that what Mylenium was thinking of is the inability to import an Illustrator file with each object on a separate After Effects layer. That would be a very good thing, and it's a common feature request. (If you want to add your voice to that feature request, please fill out the feature request form.)
If you're working in Illustrator for the purpose of bring items into After Effects, you'll really want to keep objects on separate layers in Illustrator so that you can animate them separately in After Effects.
Yepp, my mistake. I always confuse this kind of stuff. Doing too little with Illu, apparently. ;-)