How do you flip perfboard to plan where the solder connections go?

Go to View/Set Grid Size and enter 0.100". Each light grey grid intersection is where a prefboard hole is.
Click on grey PCB and in Inspector change the size to what you want.
Put the parts in the same position as on the prefboard, and click on a parts connector and drag it to the other parts connector. If you waant 90º links just grab a track in the middle and drag snap it to a grid.