Using Mail in Lion & on devices

I am using Lion and on iCloud. I have Mail checking emails to my dot.mac account as well as two others [one POP and one not, tho might upgrade that one]. My main access of mail is either my desktop or my laptop tho of course I do so with my iPhone and iPad.

I'd like to reorganize and clean out the various folders I have and emails etc. Is that something better done at the desktop or directly on iCloud? My plan is to archive the mail [maybe also using MailSteward to do so] and then consolidate or move folders to make it easier to use them.

Thanks for any practical suggestions as to the best way to do this.

And after I do the cleansing at either the computer level or iCloud, do I have to do anything special with either Mail in iPad or iPhone?? Should I just delete those accounts and then readd them after the cleansing? Thanks