I don't know if that's possible.
I managed to have conemu open two tabs (with a custom name) on startup and cd inside the folders i needs, now my question is: Is there any way to make conemu open two different tabs in two different windows and position them top-right-corner and bottom-right-corner?
The task i run on startup is the following:
title Website & cmd /k "%ConEmuDir%..\init.bat" && cd c:\src\www
title Other& cmd /k "%ConEmuDir%..\init.bat" && cd c:\src\other
Thanks