Does anyone have any efficient techniques for saving mail on more than one machine and in the cloud (I need offline access). Trying to avoid endless message copying.

Question

I've been in an administrative job at my university, in which I needed to be able to access lots of past email conversations.  I ended up saving *everything* religiously, by copying each email or conversation into an "On My Mac" folder on either my home or office machine, flagging it as copied, then unflagging it and moving it to a like folder on the other machine. As a result I'v now got a trillion folders for various aspects of my job, filled with quite a few messages that I probably no longer even need, but they're way too many to go through and delete one by one.  Unfortunately, I haven't made much use of the iCloud folders, but I'm so tired of having to essentially manually sync my stored mail in the manner I just described, that I'm thinking of starting to file everything to iCloud folders.  The downside of that is that obviously if the internet is down and a given folder wasn't refreshed before it went down, I won't have access to the saved mail.
Moreover, I'm about to step down from the admin post -- within about 6 months a lot of what I saved won't be needed at all, and going forward, I won't need to save nearly the same quantity of messages for later reference.  I'd like to come up with some viable "triage" strategies for limiting the mail I do save.  
This is really just an open question:  Does anyone have any good mail filing and storage techniques that you'd be willing to share?  I'm especially interested in criteria you use for what you save and don't save, and where/how you save it. 

Answer 1

Well, the one set up on exchange 2k3 is now working fine, although no changes were made on either the iPhone or the exchange side, so that's fun, but it still is throwing errors when connecting to the other 2 exchange accounts. The common elements are that both non-functioning exchange accounts are google apps for business accounts. So is one of the ones that's working, by the way. The settings on both accounts are the same as the one that's working, and both worked fine before the 8.3 upgrade. I have no issue accessing both of these accounts on my ipad which is currently on 8.2.x. If it's not the iphone OS at fault, I'm at a loss as to what it could be.