Inbox Problems - Mac Mail Slow due to too many messages (45,000+)???

I have more than 75.000 messages in Mac Mail (mobile me). I need all these messages and constantly refer to them - they stretch back several years. I use the search system in mail to locate the one I need, when I need it etc.
Recently I have noticed that mail is getting slow to download new messages. I have been watching the activity window and see that mail seems like it checks each message for flags/changes before downloading new mail.
I am running several Macs in several locations and need all my mail to be available on all machines - hence i se IMAP not POP3.
I am wondering if I can speed things up by moving and sorting the 45,000 messages in my inbox to folders etc. Yes? No?
Also, if I create folders, I assume that I should create these on Mobile Me (not 'on my mac')?
Thanks for any advice!
Message was edited by: Nick Syrett

I think that sorting them out to folders on the server would help this.
In Mail Preferences/Accounts/Advanced what is your selection with regard to Keep copies of messages (and attachments) for Offline viewing?
Ernie

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