The software looks at the make-break sequence to determine if the frequency should be raised or lowered. The two switches make and break in an overlapping manner as the knob is rotated. The encoder may be a mechanical or optical switch assembly, with or without detents. When it is referenced in the sketch, typically you will see which pins are used to connect the encoder assembly. Peruse your sketch and see if you can find "#include rotary" This is a library module that deals with rotary encoders. The easiest and most convenient way to control the frequency is with a rotary encoder, less than $5.00 on ebay. If yours needs 3.3 volts you may drop from 5.0 volts using two diodes in series. Be careful, as some AD9850 modules have a crystal oscillator that works fine on 5.0 volts, but others should not have more than 3.3 volts. There are dozens of implementations of DDS VFOs using Arduino and the AD9850 module like yours.
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