In addition to what Makhzumi has said, I would like to add that:-
1) I am not sure if you have to apply soil properties to all of the mat layers, but what I would prefer is to draw drop panels (thick portions of the raft) and then draw the rest of raft (no overlapping). Then as your senior told you to draw thick slabs (stiff property) fro drawing columns over column points in SAFE. But remember do not apply soil properties to these stiff elements. Make thickness of these elements as 1m.
2) You will get concentration of soil pressure and moments near supports (near columns). But do not go for the maximum peak pressure or moments.
For bearing pressure, take the contour value just at the face of the column (stiff elements you just have drawn in step 1). Do not read contour values at the edges of elements rather look for the value in the center.
3) For moments and reinforcement design, design for 1m wide strip and average the moments for 1m width. You can do this by applying design strips in SAFE in x and y direction of width = 0.5m and then replicating them every 1m to cover all of your raft. Then after running the analysis you can put in the numbers of bars or dia of bars and the intended spacing of bars to check what reinforcement you require.
Do let us know if you find more problems.