i've heard of that "onTop" problem, so I think the best and easyest way is to hide all.
Example: make a hotkey (perhaps Win+H)
than you can use a script:
*script bang !hideall
*script gotoif ("%{hidden}" = "on") 1
*script exec !varset hidden "on"
*script exec !systrayhide
*script exec !unloadmodule $dirmodulescommon$shortcut3.dll
*script exec !jDeskSetWorkArea "6,-6,6,-6"
*script gotoif ("%{tasks}" = "full") fullh
*script exec !main1labelhide
*script exec !amplabelhide
*script exec !commandhide
*script exit
*script label fullh
*script exec !main2labelhide
*script exit
*script label 1
*script exec !varset hidden "off"
*script exec !systrayshow
*script exec !jDeskResetWorkArea
*script exec !reloadmodule $dirmodulescommon$shortcut3.dll
*script gotoif ("%{tasks}" = "full") fulls
*script exec !main1labelshow
*script exec !amplabelshow
*script exec !commandshow
*script exec !detectwa
*script exit
*script label fulls
*script exec !shortcutgrouphide 1 2 3 4
*script exec !main2labelshow
*script exec !shortcutgroupshow 6
*script ~bang
you can use this script and enter your own