Re: Native formats for print?
Native .ai and .psd is what is recommended by Adobe to use, and there is no problem dragging and dropping them into InDesign. .eps and .tif are what Quark has to have placed/linked, not InDesign.
InDesign is this century. Quark is last century. As long as (in either program) you have Links and they aren't embedded (they show as a link and not showing embedded icon in the Links palette in Adobe, and Quark Picture Usage shows a link to a file), then it should be fine. Copy and pasting has been and still is a no-no (because if we don't have the links we can't fix problems that we see).
Always save out of Photoshop with the RGB profile that's used if placing into Adobe. If placing into Quark, make sure it's been converted to CMYK, grayscale, or bitmap (for black and white logo) before placing into Quark.
If in Adobe CS2, use North American General Purpose 2 color settings. You can use .ai and .psd and therefore not have to flatten live transparency. The future of prepress is PDF/X-4 and the Adobe PDF Print Engine, so Adobe already allows exporting a PDF 1.4 out of Adobe apps, while Quark still has to make PostScript. For this reason, Quark will eventually die if they don't allow export of PDF 1.4 or higher out of Quark in the near future, because with all this transparency, and because flattening transparency is not even done in an Adobe PDF Print Engine, prepress needs PDFs with live transparency intact, which Quark doesn't do. In short, prepress needs to be able to alter the PDF just like native files. The only PDF editor I've used that does this is Neo. File > Preflight to make sure nothing is wrong, then Package, using the contextual menu to Create Archive (OS X) of the "package" (folder and its contents), and send to prepress/printer.
If in Quark (if you must use it, which I recommend against), use North American General Purpose 2 color settings in Photoshop (so CMYK going into Quark is SWOP), in trapping preferences uncheck process trapping and make Auto Amount and Indeterminate to both be 0pt, link to .eps or .tif in Quark, don't use RGB in Quark at all, don't make lines thinner than .25pt, don't turn on color management in Quark 6.5 at all (and don't even attempt the mess that is 7, but if you do, only work with stuff created in 7, in 7, and turn on Proof Setup to CMYK and Spot, so that you can see that untagged RGB that's placed into Quark is assuming the wrong profile, and you'll have to manually make each untagged RGB image use sRGB IEC61966-2.1 to make skin tones to not look sunurned), and do a File > Collect for Output to get links and fonts to send to prepress/printer. Again, use the contextual menu to Create Archive (OS X) of the "collected for output" folder and its contents, and send to prepress/printer.
Hope this helps.
Don (I've worked in prepress for over 12 years now)