Prescott, a Germany youth international, plays for the Under-19s and had to get special clearance to work in the evening as a teenager ahead of a potential start on Wednesday. He is the only option should Urbig, who picked up a concussion in Bayern's 6-1 first leg win in Italy last week, not be fit.
"Jonas trained normally today. The decision tomorrow will be a medical one," Kompany told a press conference.
"If everything goes well, then Urbig will be in goal. If not, then we will have to find another solution.
"He (Prescott) is very calm. Overall, we as a staff are also calm. If he plays tomorrow, he will have our full backing.
"Everyone will help. There will never be a young player who will be forced to play a main role," Kompany said. "We have full confidence in him, whatever happens tomorrow."
Bayern are without first-choice keeper Manuel Neuer, who is working towards a comeback but is not fit yet.
Third-choice keeper Sven Ulreich joined Neuer and Urbig on the injury list after picking up an adductor muscle problem in Saturday's 1-1 Bundesliga draw at Bayer Leverkusen.
The Bavarians have no plans to play it safe despite their big advantage in the tie.
"You cannot allow too much. We made such an effort to build up the momentum we have," Kompany said.
"This is not a friendly match... and if it is not about the result, it is about performance."
Atalanta or Bayern, who lead the Bundesliga title race and are through to the German Cup last four, will face Real Madrid or Manchester City in the last eight.