how to sort your emails?

for quite a while i'm sorting my IMAP emails with a sieve script on the hosting server. this works great and suits me quite well, because the sorting happens independent of the location where i read my mails.
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the script kicks in and files the emails in different folders when they come in. this leads to the main disadvantage: the notification system of many email applications is for subfolders rather flaky. (apple mail works surprisingly well, mozilla thunderbird is quite bad and on the iphone it doesn't work at all!)

therefore my newest plan is to let all emails come in the inbox and file them by a sieve script after they're marked read. i guess this would mean that a script checking and filing the read items in the inbox is trigger periodically.

another benefit would be that the inbox gets emptied after i read an email, so if i want to keep an email in the prominent inbox i just ned to keep it unread.

however, i'm not sure yet what arcitectual setup i would need to achieve this...