Break it down,
"Since you did the last project very well, we are going to give you another project"
"Since ......., ........."
This usage should be familiar to you. This means that because the person has done something in the past very well, he/she can be entrusted with additional tasks"
"You did a fantastic work (at) running the project" means the person did a fantastic work getting the project to run and maybe even maintaining its smooth function."
Just combine the two together and you will understand it completely :)