When editing or creating a rateplan you can select what upgrades are included in the nightly rate.  These are not added to the checkout and will not show up as purchased upgrades on bills or confirmations.

The price for the included upgrade(s) will be deducted from the rate for that night.

Select the upgrade to be deducted from the nightly rate and save the rateplan.  In the example below, breakfast is being added to the Bed & Breakfast rateplan.  Breakfast is €10 per person per night.  So for every person in a room, €10 will be deducted from the nightly rate.

When running a Revenue Report the nightly rate will also be shown without supplement.  Below you can see the Bed & Breakfast night rate is €69 and without supplement the rate is €59.
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When running a Daily Room Recap report you can optionally exclude supplement from the nightly rate.

The nightly rate changes depending on if the supplement is to be included in the night rate or not.
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N.B. If the nightly rate is 0 or deducting the supplement from the nightly rate would result in 0, then the supplement will not be deducted. 

Example:  The rateplan/special offer is "B&B plus 2 Dinner" and the min stay is three nights.  So the rate includes 2 dinners per stay and 1 breakfast per person per night.  You would click the "Dinner €40 per stay" upgrade and make the number of that upgrade 2.  You would also click the "Breakfast  €10 per person per night" and leave the number as 1.  
Each night rate would then automatically be reduced by