in Safe , you have to provide value of modulus of subgrade, you can't define bearing capacity.
Geo technical report should mention actual modulus of subgrade , otherwise you have to do it on the basis of load and allowable settlement. ( BOWLES - Foundation Analysis and design)
As you have mentioned that you are new in this field, you should concentrate on manual calculations, it would be utter madness if you simply accepted your software results without any manual checks and without any involvement of your engineering.
if you are giving 48 inches raft for 5 storey building, it is too too much ( if it is commercial or residential), it means your loading ( live and dead loads) need correction. verify them from UBC OR ASCE.
Calculate Punching manually first.