Shopify's multi-location feature supports inventory in more than one physical location.
Single & Variant eBay Listing Default Location
The eBay channel links to whichever location has the highest amount of inventory available by default for single item listings. For variant listings, by default, the inventory location in Shopify is used that has inventory available for all variants. If two or more variants have quantity available for all variations of the product, by default we will link to the location that has the most quantity available.
Editing Linked Location for eBay Listings
You are able to edit the linked inventory location of an eBay listing.
eBay Order Sync
Orders will sync to reduce quantity to the linked inventory location within the Shopify product. You are able to change the fulfillment location prior to fulfilling the order within Shopify. Please refer to Shopify's documentation on fulfilling orders with multiple locations.