How this works depends on which version of Make an Offer you use.
Latest Version (V2+):
For product offers, only the product with the accepted offer will appear in the checkout. If a customer has offers on different products, they’ll get a separate checkout link for each one.
If you want customers to make offers on an entire order, set up an order offer. When creating a new rule, select Order under Offer Type in the Conditions section.
Legacy Version (V1):
If a customer submits offers on multiple products, you can combine them into a single order offer:
In the Make an Offer admin section, click the Offers tab.
Find and accept one of the offers.
If the customer has made more than one offer, you’ll see the option to combine them.
Select the offers you want to combine and click Yes.
In the next window, choose whether to accept or counter the combined offers.
Click Done.