Dynamic alignment guides
When you drag activities to move them, alignment guides will automatically appear in the canvas. You can also use the arrow keys to move single activities, but the guides don’t appear.
Alignment tool options
Alternatively you can highlight multiple activities and use the ‘align and distribute’ icon on the top bar to quickly tidy up diagrams. Note that you need to select a reference object, and then (on Windows) shift-select the rest or (on OS-X) cmd-select the other objects.
Sizing tool options
The next icon to the right allows you to quickly match height and/or width of activities (again, select your reference activity, and then ctrl/cmd select the scope of activities to match).
Note: In both cases you can “drag select” a range of objects, but if that re-selects your reference object, it will change the size/alignment to the lowest numbered activity box. So, select and ctrl/cmd drag works, but only if you are not re-selecting the reference.
The activity box numbers don’t have any meaning, but they do form the basis of level numbering and visual appeal, as people normally like to see the completed diagram with some logical numbering. In the Pro version there is rules based renumbering functionality based on alignment (top to bottom, left to right).
In the free version, you can still renumber, but it is manual.
If you right click on an activity box, select "Change number". If you use a number that is already in use on another activity they will be swapped.
This simple approach makes it less of a mind-game puzzle and a little less painful: