Line commands (often simply called commands), are instructions to change, insert, and delete characters or records (see above copy or change), to position the current line, to load and save workfiles, and to apply a variety of other functions. Actually, you can enter (line) commands anywhere in your window but usually you will use the dialogue zone.
Prefix commands are commands to insert, delete, copy, and move lines. Prefix commands are written in the data zone in the prefix area (see picture in Window Mode and Line Mode) at the beginning of each line (where the line number is located).
The main principle of feeding data in exaEdit is that anything you have typed in remains without consequences and is still changeable until you press the return key. Only then will your input be processed.
For your input, which you hand over to exaEdit by hitting the return key, you are allowed to combine the three options discussed above without any restrictions - although not every combination makes sense. But frequently it is an advantage to enter direct changes and prefix commands simultaneously by pressing the return key only once.