Many of the banks in our holding company provide customers a change-in-terms notice via a statement stuffer. How do banks handle this when the customer no longer receives a paper statement? Would it be acceptable to include the statement stuffer as an attachment in the email which the customer receives notifying them that their e-statement is available?

The e-statement agreement does include language stating that the customer not only agrees to receive periodic statements electronically but also other disclosures, notices, etc.

We handle it as a popup when the customer logs on to online banking. They can view the info or say no thanks to continue to their account.

If your customer has demonstrably consented to the use of a particular technology, then that's the only technology that gets the ESIGN seal of approval. In order for e-documents other than statements to be treated as "in writing", they must be included within the scope of the consent and delivered in accordance with the consent's hardware and software requirements. General notices and other content that does not have to be "in writing" can be handled any way you want.