Which fungi? Are you trying to make yeast recomibation library? And over expression of particluar cassette? There are many protocols however it needs to be optimized for your cluster.

i think you should use recombinant but you can also use site directed mutagenesis. in which you can enginering the pathway of the enzymes for production antibiotics/vitamin by blocking of the feedback inhibition using SDM techique for regulation domain of the enzyme. or you can use recombinant, that you must insert cloning and expression vector that has strong promoter, and high copy number vector...

Pichia would be a good choice to start with