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I went bare bones with my email system when I got my iPad. Like you, I have multiple accounts to juggle. In each account I created folders, on the server, for Archive, @Action, @Quicken (for bills, receipts, etc.), and @OfflineArchive.

Every email eventually lands in one of the archive folders. Messages in Archive remain on the server for access from the cloud. Messages in @OfflineArchive are moved to an OfflineArchive folder on my Mac when I happen to do my evening review there (mostly these are mailing list messages). Every 6 months, I'm moving the messages from 6-12 months ago out of the archive folders and into EagleFiler.

The @Action messages get processed into OF in my evening review. The @Quicken messages get processed once a week or so. In either case, once I've processed the message, it goes to Archive.

I use some custom scripts and FastScripts on the desktop to push the messages around using hot keys. I also use some smart folders to show all the @Action folders from every account in a single group, and similarly for my other folders.

This design works great on the Mac and OK on the iPad. I still have to walk through the different @Action folders on the iPad, and copy-and-paste email text into new OF actions. It isn't ideal, but I think it's the best we can do at the moment.

I've given up on automating waiting - from email, and did so long before getting my iPad. Everything I'd tried was too fragile and I realized that I wasn't gaining enough in automation. So, now I just Quick Enter a new @waiting action after I send the email.