in the retarget manager for the skeleton you are retargeting from take him and mode him into the same T or A pose as the mesh that you are retargeting too and then click the save pose button and it will use that as the default pose when transferring the animations
Thanks for your resoinse James. I know that and I get it working.
The problem comes when i retarget using a pose and then I need to retarget again but from other source pose, and more times. This end up being a pain.
So I am asking is there is an elegant way to manage this.