You can add comments and save alternate lines in any game that you open in the analysis board! You can get there either by running a game review and then going to the 'Analysis' tab, or click on 'Analysis' under the moves list.

To add comments or icons to a move, simply right click on the move in the analysis:

Choose Comment Before or Comment After to add a text comment before or after the move you have clicked on. Or, click on any of the icons to add that icon to the move. You can also do both of these options:

To add a variation, simply play out the alternate moves on the board. You can also comment on the moves in the alternate line by right clicking on them:

If you make an incorrect move, simply right click on that move, and you can delete it, or delete the whole variation:

Once you have added all your comments and variations, just click on Save below the moves, and the analysis will be saved into your Saved Analysis folder!