Greece clawed their way back against the hosts for a 1-1 draw after conceding an early goal and having a man sent off in the first half.
The Greeks must also play the Czechs without their first-choice central defence.
"Whenever the going gets tough they manage to perform well," Santos told reporters on Monday. "We hope there will be no need for difficulties to show up for us to play our best."
Santos must find replacements for Avraam Papadopoulos, who is out of the tournament with a knee injury, and Sokratis Papastathopoulos who is suspended after being harshly dismissed against Poland in the Group A opener.
Veteran midfielder Costas Katsouranis will likely anchor the back-line with 20-year old Kyriakos Papadopoulos who came on for his namesake against the Poles.
That could open a spot for midfielder Giorgos Fotakis to start should he pass a late fitness test after picking up a knock in training.
"I want to be clear that if Fotakis can't make it Greece has many alternatives to build up a very good starting XI," Santos said.
The Czechs also face defensive problems after Russia ripped them apart with four goals but Santos was coy when asked whether he would seek to exploit that weakness by adopting attacking tactics.
The Portuguese coach added that he expected a strong Czech side to take the pitch even if his counterpart Michal Bilek makes changes to a side that rarely troubled the Russian defence.
"From our part we have analysed the Czech team and we have done our homework with respect with what we have to do," Santos said.
"What we must do is focus on the qualities on our team and the way we played in the second half."
Russia play Poland in Warsaw in the other Group A match on Tuesday.
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