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I asked a question like this a while ago... basically it has to be done for each user manually (either by them, or by you).
Alternatively, you could change the SQL tables, but it's not a simple case of changing a 0 to a 1 for every user. Each notification is a row (OK I don't know the real name) in a notifications table, so you'd have to know how the notifications system works (e.g. whether other rows are affected; what the column headings represent - this bit is easier) then add lots of rows, or use a modified php script (notifications.php?) to run through all users and add rows for each of them (and for each module).
Hope this helps.