Which ever account you want it to delete on both the handheld and the mailbox. If you go to messaging services and change the account up there, it will give the options for each account. If you want all your accounts to delete on both. Set all the accounts that way.
If you have your device email (not sure what you mean by that. Maybe you're on a BES and it is your corporate email) set to prompt but your yahoo is not, any email you get from yahoo will not prompt or delete on both. I would check the setting for all of your accounts to verify they are set how you want them.
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