If I understand the problem correctly try this:
Right click on the dock and choose SETTINGS
A box should appear with two tabs, one of which is HOME
Your dock should appear there, and then pick ACCESSIBILITY
Then pick REGULAR and SHOW DOCK WHEN MOUSE TOUCHES EDGE
That should put the dock in the background when other programs launch, and bring the dock to the foreground if you put your mouse against that adge of the screen.
