First of all, be super careful about the terminology. Epicor used to call sites “plants”, which you can still see in database column manes. They changed plants to “sites”, but there was already something called “multi-site” that referred to the physical location of the servers in a multi-company setup. If you start reading the docs about “multi-site” and find yourself very confused, that’s why.
Most of the multi-plant issues I’ve run into are related to the configurator. Transfer orders cannot carry a MoM or configurator inputs, so you cannot set up configured parts as transfer. (Unless maybe you’re using the options to create part master parts, which I’m not.) The configured items have to be manufactured and shipped from the manufacturing plant. This is fine for drop-shipping to the customer. Otherwise, set the OTS address to the store. The product sits there untracked until the customer picks it up.
As mentioned, revisions (and therefore MoMs) are site-specific. This is a problem if you’re quoting things in a retail site, because the UI won’t let you run Get Details for a part manufactured in another site. But in a BPM, you can call Get Details cross-site by creating a temporary context changed to the manufacturing site. I’m doing this in a post directive on the last method called when a quote line is configured. Side bonus, the guy behind the counter just has to click the Configure button. He doesn’t have to (and in fact can’t) run Get Details from the menu.
When the quote is converted to a sales order, OrderRel.Plant should be set to the manufacturing site, not the retail site where the order was placed. This creates accounting issues that I haven’t delved into very deeply myself. My limited understanding is that OrderRel.Plant is what actually controls which site receives the revenue.