You need to have the development version for that (e.g. from
http://hgm.nubati.net/winboard0526.zip ); 4.4.3 does not do variations yet.
To enter a variation simply enter the main line first (in edit-game mode), then use the < and > buttons (or arrow keys) to step through the main line to the move you want to play a variation on, and simply play the moves of the variation from there. This will make WB shelve the tail of the main line. When you are done entering the variation, you can use the Step->Annotate menu to return to the main line. The variation will be added as a PGN variation comment (i..e. in parentheses) to the move where you branched off. This will be visible in the Comment popup window. When you later save the PGN, the comment will saved with it.
When you load a PGN containing variations, they will show (together with other comments) in the Comment popup. (You would want to make sure that /autoDisplayComment=true.) The < and > will step you through the main line, and show the comments for the move where you currently are in the Comment popup. If you want to follow a variation, right-click it in the Comment popup on that variation. (One move can have more than one variation on it.) This brings you to the move where the variation branched off, after shelving the main line. With <, > you can then step through the variation. This time you should use Step->Revert to return to the main line, because the variation comment already existed.
That is really all. And it works recursively (variations on variations).
There is some limitation in the level of nesting the parser can handle when it reads PGN, though (I think three levels of nesting beyond the main line). The level of nesting you can use internally (and then write) is much larger (16, I think).