The difference of both minerals can partly be seen as different degree of crystalization – usually crystals are better expressed at kaolinite than montmorillonite, and the syngony is slightly different. But this differentiation is usually difficul, therefore you better use EDS mode, and difference in chemical composition will for sure help you to differentiate the two minerals. Kaolinite contains much more alumina (around 40 % Al2O3) than montmorillonite (around 20 % Al2O3, together with some sodium and calcium). You can easily find some more data on the web (webmineral.com).