In order to reconfigure an iPhone to keep the sent, drafts or deleted messages on the mail server, you should first login to the e-mail account through the built-in iPhone mail client and then browse the following folders:

Drafts Mailbox
Sent Mailbox
Deleted Mailbox

Next step is to open Settings -> Mail, Contacts, Calendars -> Select your email account -> Select the displayed IMAP account -> Advanced Settings (at the bottom) - > Mailbox Behavior.

You will find the following 3 options listed at the top:

Drafts Mailbox
Sent Mailbox
Deleted Mailbox

Each of these options lead to a page that allows you to configure your phone in which folder to store a copy of the respective messages. Each page will display a directory tree from the server, and you need to mark one of the listed folders, under the "On the server" section in order to force the mail client to store the messages there.