The workshop is a building that let you buy permanent upgrades by using the blueprint points, which is made by using the factory or exchange 100 special resource for 1 blueprint point.
Offensive upgrades are uses to make it easier to kill your enemies. (I.e bigger attack range,faster firing speed)
Defensive upgrades are uses to make that you will still be alive after taking hits by multiple means (I.e more hit points,block amounts)
Utility upgrades are uses for making upgrades and getting random resources easier to get (I.e the random offensive upgrades,resources/waves)
The ultimate upgrades are available when you reach tier 1, you can get more available when you upgrade tiers. The ultimate upgrades are some of the most powerful upgrades of the game. (I.e turning elemental into basics white enemies.)