I have an iPad 3 and want to do the same, transfer magazine issues from iPad to iMac desktop. SOme of the issues from New Yorker and Scientific American are huge, 150 MB to 600 MB - I can see the iPad filling up quickly.
Some posts on other forums and info from the publishers suggest that we might like to delete issues and re-download them if we need to later.
Frankly that stinks, I'm damned if I want to waste my monthly data plan re-downloading stuff that I already own, why can't I simply archive older issues on my iMac?
This is a case where DRM is just insane, if I own a paper copy of a magazine its always there for reference and for lending to family and friends. And considering that many digital editions of magazines cost the same as hard copy editions I think its a disgrace.