you will be able to place an order over the phone at any mbmj store, but they will have to send you an authorization form first where you'll have to provide them with your shipping and payment information before they can send out your items. shipping will be a flat rate of $20, so you should order everything you want all at once.
the jacobs by marc jacobs totes are available at the mbmj boutiques in navy blue and black depending on what they're stock is, they should have both. i am most familiar with the nyc store, and all the canvas bags are available there as are most of the special items on the website.
i went the other day and couldn't find the jacobs by marc jacobs tote i was so sad but they did have a cute white marc jacobs tote (it was different-just said marc jacobs on it)-but i'm holding out for the navy blue jacobs one