The SmartVault (SV) connection on a Method account is company-wide. This means that anyone accessing the Upload Attachment… screen via the account in question will be able to select the upload to SmartVault option.
I don’t have a SV account to test this myself, but this should function the same way via the portal.
Keep in mind that the Upload Attachment… screen is one of the few screen in Method that cannot be customized. This means that you won’t be able to force your clients to upload to SV via the portal. You may want to include a note for your clients, in your portal, indicating that they need to select the SV option.
I hope this helps.