What each endorsement covers
The 2-wheel endorsement is the standard one, and it lets you ride conventional two-wheel motorcycles. The 3-wheel endorsement is for three-wheeled machines: trikes and the increasingly popular can-am style rides. They are separate, because balancing and steering a two-wheeler is a genuinely different skill from controlling a three-wheeler.
Which one you need
Simple rule: match the endorsement to the machine. If you ride or plan to ride a standard motorcycle, you need the 2-wheel endorsement. If your ride has three wheels, you need the 3-wheel. Some riders get both over time. If you are unsure what suits you, the difference in handling is exactly what a course is for.
The course for each
WMST trains for both. The 2-wheel endorsement course is the path for standard motorcycles, and the 3-wheel endorsement course is built specifically for trikes. Both include the testing that waives the DOL exams, so finishing the right course earns the right endorsement.