You're not alone. Aside from the addition of a swipe card reader and of the SmarTrip pad over the years, the user interface of WMATA's farecard vending machines is definitely atrocious, especially for a city and system that sees such a large number of tourists. The situation has been made even worse because of the addition of the $1 surcharge for paper farecards (and the deeply unpopular experiment with "peak of the peak" surcharges). The software is more than 20 years old and has had security problems as well.
DC Metrorail fares vary by distance and time of day; there is no such thing as a "single trip" or "multiple trip" farecard. Whether using the WMATA SmarTrip card, Baltimore Charm Card, or a paper farecard, you're simply adding cash value to the card, which gets deducted electronically when you exit the platform at your destination. Don't think of the farecard as holding a certain number of trips, as it would for instance in the New York City Subway.
At the stationmaster kiosk you'll find a table that gives you the regular (rush hour) vs. off-peak fares for every possible destination from the station. (The list at the top of the machine is for paper farecards, and includes a $1 surcharge). Let us suppose, for simplicity, that you are traveling on a weekday morning from Virginia Square to McPherson Square for a breakfast meeting, departing at 7:00am and returning at 9:00am. The fare during those hours is $2.50 each way. You have a SmarTrip card with $0 stored value.
When you tap your card onto the pad in front, it will ask you how much value you want to add, with a default of $20. This is what the "add value" and "deduct value" labels refer to. If you only want to add $5 to the card, press the down buttons until the value on the display reads $5. If, on the other hand, you want to add $50, press the up buttons until the display reads $50.
Then, when ready to pay, insert the required funds, whether by credit/debit card or by adding cash bills or coins.
The 1996 Washington Post guide offers a screen-by-screen guide, but it predates SmarTrip, the elimination of paper farecards, and almost two decades' of changes to the fare and pass structure. I could not find anything better.