Let's say you have items in inventory as
(Burger Categories)
Hamburger $1
Cheeseburger $1.5

(Pizza Categories)
Cheese Pizza $2
Sausage Pizza $3

(Fries Categories)
Small Fries $0.75
Large Fries $1.50

(Drinks Categories)
Coke $0.50
Sprite $0.50

You want to create:
Combo A (Hamburger, Small Fries and Coke) for $2 (Not combo is $2.25 total)(This is specifically set the items for the Combo)
Combo B (Cheeseburger, Large Fries and Coke) for $3 (Not combo is $3.50 total)(This is specifically set the items for the Combo)
Combo C (Select 1 from Burger Category, Select 1 from Pizza Categories, Select 1 from Drinks Categories) get $2 discount from the total. (This is NOT specifically set the items for the Combo, but let customer choose the items in the each categories)

Currently for Clover to have Combo is to create an item call
Combo A with modifier (just for) Hamburger, Small Fries and Coke and set the price to $2
Combo B with modifier (just for) Cheeseburger, Large Fries and Coke and set the price to $3
Combo C with modifier of Burger Categories, Pizza Categories and Drinks Categories. You have set the price of each modifier already discounted so the total comes to your expectation.

But, there are some major problems to this method.
At the end of the month, you CANNOT run an item sales report to see how many burgers, fries or coke you sold. You CAN'T run the report of item sold for just Burgers. You have to check each modifiers of each items and manually count how many of those items sold. You also can't run discounts when the # of items in the combo requirement are meet.

The correct method of doing this is to have this thing call Combo in the inventory, where you can create a name for the combo and select either Categories or individual items into it to create a combo that you can set discount by $ amount or percentage off and with date and time this combo can be available. (example: BOGO M-F from 12p to 4pm only or BOG2ND50%OFF During whole month of March All days)

(The Clover app "Mix, Match or Combo" does this already very well on the Clover register, but it doesn't work for Clover online orders)

When you run the item sales report, you can tell how many of each items were sold. NO MORE going into each items to count modifiers manually.