The protists with flagella; move by beating their long whip like structures called flagella. They can have one or more flagella that help them move. Many of these type of protists live in the bodies of other organisms.
On the other hand, protists with cilia; move by beating these tiny hair-like structures (cilia). The cilia act as tiny oars that allows the protist to move through its watery environment. The cilia also help the protists capture food particles. Therefore; both are able to move food particles towards themselves using the respective structures.