Much navigation will be done with the scroll bars and the mouse but you can also navigate with the keys. If you click into either window then you can use the cursor buttons left, right, up, down, page up, page down, home, end, ctrl-home, ctrl-end as you would in other programs. The overview-column next to the vertical scroll bar of the input files can also be used for navigating by clicking into it.
You can also use the wheel mouse to scroll up and down.
In the merge output editor you can also use the other keys for editing. You can toggle between insert and overwrite mode with the insert key. (Default is insert-mode.)
A left-mouse-button-click into any summary column will synchronise all windows to show the beginning of the same group of lines (as explained in section "Setting The Current Group And Synchronising Merge And Diff View Position").
The button bar also contains nine navigation buttons with which you can jump to the current/first/last difference, to the next/previous difference (ctrl-down/ctrl-up), to the next/previous conflict (ctrl-pgdown/ctrl-pgup), or to the next/previous unsolved conflict. Note that for KDiff3 a "conflict" that was not automatically solved at the start of the merge stays a "conflict" even if it is solved. Hence the necessity to distinguish "unsolved conflicts".
There also is a button "Automatically go to next unsolved conflict after source selection" (Auto-Advance). If you enable this, then, when one source is selected, KDiff3 will jump to and select the next unsolved conflict automatically. This can help when you always want to choose one source only. When you need both sources, or you want to edit after selecting, then you probably want to switch this off. Before proceeding to the next unsolved conflict KDiff3 shows you the effect of your choice for a short time. This delay is adjustable in the Diff- & Merge-Settings: You can specify the "Auto-Advance delay" in milli seconds between 0 and 2000. Hint: Tired of many clicks? - Use a small Auto-Advance-delay and the shortcuts Ctrl-1/2/3 to select A/B/C for many conflicts.