How are Antimicrobial agents applied?

Depends on the situation and the agent. Technically, "antimicrobial" should be used synonymously with "anitbiotic" -- an adjective that modifes a type of medicine. In this case, meds can be injected (IM, SubQ, IV, IO, IC etc.), orally (PO or SL), topically, by suppository, etc. If you mean antiseptics, these are topical killers of infectious organisms. These include alcohol, hydrogen peroxide, betadyne, and a wide variety of soaps, gels and creams, all designed to attack organisms that are topologically outside the body. They can be poured on, scrubbed or sponged in, squirted on under some pressure, appied with a Q-Tip, sprayed on as an aerosol, etc.