I am assuming that you are doing all-grain or partial mash, where the following will apply:
If you want to keep back a gallon of trub and wort in your kettle, this is captured in the 'Loss to Trub and Chiller'. The loss to mash tun dead space covers losses before the boil and so that volume will not impact the IBU calculation or gravity calculations for pre boil estimates.
Now having said that, adding your loss to trub and chiller will not affect the way the program calculates your original gravity and, hence, ABV. This value is calculated based upon the brew house efficiency you specify in your equipment profile. Brew house efficiency (BHE) is a variable in the process that the user fixes as a constant and it determines the amount of sugar from the fermentables bill which make it to the fermenter. Since this value affects the gravity going into the fermenter directly, any change in volume losses within the process will result in the program forcing more sugars from the grist. If you look at your estimates for mash efficiency when you add your gallon of trub loss, you will note that this estimated value will increase as you create a greater loss of sugar in the process and the program extracts more sugar from the grains to fix this loss of sugars.
The best way to make the change you are anticipating is to note your post boil volume before you make the change. Now, make the change in the trub loss and note the increased amount of post boil volume. Take the BHE from your equipment profile and ratio it based upon the increased boil volume. So you will end up with the equation: BHE * old pre-boil volume / new pre-boil volume = new BHE. Now change the BHE in your equipment profile to match this new value and you will get an appropriate estimation of your OG and ABV due to the change you are making in your process.