We've put together a guide to doing this - it will involve duplicating items and changing how they appear. Then from your Manager's account, under the menu tab, you will need to turn off the items that don't need to be displayed on your online ordering. It will take some time to do but once finished, you will have two separate menus.
You will need to do this through the Inventory section in the web app/on a desktop computer.
When you are in Inventory, you'll first go to Items, and you'll be given a list of every item in the menu.
You'll see on the right-hand side, there are a few icons, you'll click the middle icon (which looks like two squares) to "Clone" this item. It will create an exact duplicate of the item with all the same modifiers/options/etc.
You'll tap on that new item, and on the next page, uncheck a box that says "Show in Register"
You can change this item however you need to - for instance, if the items online have a different price from ordering in-store, you can set the price on this new item and that will ultimately be what shows up online.