Check out Keeling, B. L. 1982. Seedling test for resistance to soybean stem canker. Phytopathology 72:807-809.
This technique is fully explained using Diaporthe caulivora pathosystem I have used it for sorghum stalk rot from Fusarium moniliforme. It is adapable to greenhouse and field environments.
The inoculum is produced in leached sterilized toothpicks which are infused with potato dextrose broth and inoculated with in your case Macrophomina in 2 to 3 weeks I would expect the toothpicks will be colonized with fungus and sclerotia will be present. The test plants are pierced with a sterile dissected needle and then the toothpic is inserted tranversing the stem. You may want to periodically get incidence and severity ratings and look at the epidemic curves compared against a range of cultivars.