You can apply a journal note (with or without a flag) on multiple parcels at once.
To make a selection based on a map shape, start by drawing the map shape using the polygon tool on the map menu bar.
Click on one of the corners of the polygon you would like to draw, and then click on each of the rest of the corners and close the polygon by double-clicking on the last corner.
Go to your Parcels window pane.
In the Parcels Query Tree, find the Map Shapes node and expand it. You should have at least one option that says Custom Polygon (x) (if you still have other polygons selected on your map, they will all be options - select the one with the highest number to get the most recent one).
All of the parcels within or overlapping your polygon will be shown in the grid. You can select all of them at once by going to the Selection menu on the grid's menu bar and choosing Select All Rows.
All of the rows should be highlighted light blue once they're selected.
On the Edit menu on the grid's menu bar, choose Notes and Flags.
Click OK on the pop up that says "Only Parcel Notes and Flags present on all parcels will be displayed" in order to open the Notes and Flags form, and then click Add Note.
The same note will be added to every parcel you have selected currently.
To edit the note simultaneously on all parcels, for instance to change the type of flag, make sure that all the parcels you have selected have the same note attached.