You're being trained in how to use a computer program at work. Your coworker shows you how to do something. You respond to show that you understand.
"Got it" means "I understand." You say this when someone is giving you instructions or teaching you something:
A: That piece goes over here like this, and this piece screws into the top.
B: OK, got it.
You can think of "Got it" as a shortenened version of "I've got the idea (of how that works / of what to do / etc.)"
"Got it" is more casual than "I understand." So, for example, you would use "I understand" if you were being yelled at by your boss for doing something wrong:
A: You should not have done that without checking with me.
B: I understand.