When you start the initiative by pressing the 
button, it will change to green 
. Also, d20Pro will ask if you wish to "Roll new initiative?" If you select "OK" it will roll an initiative for everyone in the Active Roster and report the results. If you select "Cancel" it will keep the previous initiative roll and start the combat.
Next d20Pro will bring up the Set Initiative Window which will allow you to approve or change any position.
When you press this button in the middle of two creatures, it will change the lineup for those two creatures.
If you single-click on any creature on the list a popup window will appear that will allow you to manually enter in the initiative for that selected creature. When you change the number and select OK, it will make the appropriate change inside the Set Initiative Window.
In this example, we will change Valeros' initiative from 20 to 18 (this number is the total roll+bonus). And now notice the change below.
Once you have the initiative as you want it, press the "OK" button to allow initiative rounds or combat to start.