Copy/Paste graphic w/drop shadow to indesign - loses transparency

See above image.. I made a vector version of our company logo in illustrator (all programs referenced are cs5 btw) and it looks great, but when I copy and paste from Illustrator to InDesign, it loses the transparency around the logo. If I place the logo instead, it works fine. The trouble is there are about 16 variations of the logo, and its MUCH easier to copy/paste from one aggregate file instead of having many different logo files to place.
Background on how the logo was created: The inner circle area is multiple different gradient layers (some with transparency masks as well). The white line around the outside is an expanded stroke, and it had a drop shadow effect applied (Stylize menu), which I expanded so it would scale properly when scaling the logo up and down. Here is a link to download the logo: download logo
Q: Is there any way to make InDesign preserve the transparency when I copy and paste?
Would be eternally grateful if someone has a solution that allows me to copy/paste!

I agree with Bob's suggestion to use separate "layer groups" in your logo file for different styles. I also use separate layers inside InDesign to "multi-purpose" company documents with different backgrounds, graphics, and content. But that's the only way I use layers inside InDesign – Not for general placement of image files! I also disagree with ability to copy and paste graphics from Illustrator with drop shadow. Here's an .ai logo which I quickly added Drop Shadow to in Illustrator CS4, and then a Copy and Paste into InDesign CS4 document. Best workflow practice is to 'Place' image files as Bob suggests, linking them from a separate file folder.
For something "quick and dirty" I see no problem with Copy and Paste, but your success may vary based on OS, and CS versions you are using!  Sometimes it is wiser to take a few shortcuts to hit rather than miss that deadline!

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