Yep, when you look for subject-verb agreement, you are always looking to make sure that the SUBJECT agrees with the verb... and you can and should disregard any other nouns that are not subjects. In the phrase "the increase in unemployment rates is discouraging" (for example), that whole phrase "in unemployment rates" is a prepositional phrase. A prepositional phrase is a preposition + the noun that follows it, and that noun is called the "object of the preposition." The reason it's good to remember that terminology is just that it will remind you that that noun is an OBJECT, not a subject, so we disregard it when we go about ensuring SUBJECT-verb agreement. You can literally pretend prepositional phrases don't exist when it comes to subject-verb agreement: imagine the sentence without it ("The increase is...," not "the increase are...").

You should certainly practice ignoring those prepositional phrases, because throwing them in to confuse you is one of the GMAT's classic tactics!

What about this:

The Company bought their....
Versus
The Company bought its...

"Their" is plural so the first sentence is incorrect, correct?

Yep, exactly. Company is singular, so the pronoun that refers back to it must be as well: "The company bought its..."

yes, "is" is correct