looking at the message you got, I'd have to say yes
I think since MyColors has limitations (only applies my colors) and the WB trial has limitations (can't use per pixel skins on downloaded skins, only on the one's provided) they get in conflict
When I had AlienGuise before, I already had ObjectDesktop so when I installed it I got a message asking if I wanted to use the AlienGuise theme manager or Stardock theme manager
Before it was called MyColors, AlienGuise used a licensed OEM version of the applicable apps needed (WB, Iconpackager,etc)