As far as the tax code is concerned, it doesn't matter what account the money comes from. As sole proprietor, it's all your own money no matter what account it is in, so there is no reason for the SEP-IRA custodian to care. Their only responsibility is to report the contribution on Form 5498 as a SEP contribution, which they will do by default when your IRA account is marked in their system as a SEP-IRA account.
The custodian generally has no involvement in you setting up your SEP plan itself since most simply rely on you to establish the plan yourself by preparing Form 5305-SEP and keeping it in your personal tax files.
